I pretty much agree with your list Brian! Seems we grew up in the same era! I never watched Transformers though beyond it´s initial season but I always thought Megatron was the leader of the Decepticons...So I learned something. So I would erase this guy from my list and put in Bane...

Not a whole list, but I've always thought Beast Wars Megatron is one of the most complex villains I've ever seen in any pop culture medium.

-JJJ

Michael Corleone
Jaws (the shark)
Hans Landa
Mr. Blonde
Stansfield (I couldn't recall, the character's name. Gary Oldman from The Professional)
Cobra Commander (from Larry Hama's Marvel run)
The Terminator
Vic Mackey (Michael Chiklis from The Shield. I'm not sure if he's an anti-hero or a villiain.)

I apologize in advance if any are not always the villain, but, I do enjoy when you can kind of see their side of things:
Personal Favorites:
Dr. Doom (Even if I don't always keep up with FF, Doom has proven himself to be one of the most formidable villains in the Marvel Universe.)
Loki
Doctor Octopus
Starscream
Bludgeon
BW Megatron
Shockwave
Darth Vader
Skeletor

Top Ten Favorite Fictional Villains (non-Lee edition)

The Magus - Adam Warlock's evil future self, and the character I most want as an action figure.

Sinestro - Particularly during the Sinestro Corps War.

Skeletor - The Overlord of Evil was amazing in the 2002 MOTU cartoon.

The Master - Arch-enemy of the 3rd Doctor and played by Roger Delgado.

King Ghidorah - A three-headed golden dragon that breathes electricity. Arguably Godzilla's nemesis.

Galvatron - Forged by Unicron, he's so hardcore that he finds lava relaxing.

Kang the Conqueror - One of the best villains of all TIME.

Aku - The nearly all-powerful antagonist in Samurai Jack, brilliantly voiced by Mako.

Dr. Horrible - NPH at his best. Still hoping for a sequel.

Mr. Blonde - Psychopathic sadist and a fan of 70's music.

And here is a bonus list of the top ten fictional villains portrayed by Christopher Lee, in chronological order by film:

The Creature (Frankenstein's monster)
Count Dracula
Kharis the Mummy
Fu Manchu
Edward Blake (essentially Mr. Hyde)
Count de Rochefort (from the Three Musketeers)
Lord Summerisle (from the Wicker Man)
Scaramanga (The Man with the Golden Gun)
Saruman the White
Count Dooku

Rasputin the mad monk would have made this list, but he was disqualified for being based on a real person.

In no particular order...

Dr. Doom -- Greatest comic book supervillain of all time. All others pale in comparison to Doom.

The Joker -- Batman's arch nemesis, and probably the greatest non powered comic book villain. Every time the Joker is involved in a storyline, the stakes automatically become that much higher.

Lex Luthor -- Despite having no powers other than his incredible intellect, he still gives Superman a run for his money every time he comes up with another evil scheme. If anybody should have killed Supes off, it should have been Luthor and not a bony Hulk ripoff like Doomsday.

Dr. Octopus -- You can keep your Venoms and Green Goblins. For me, Spider-man's best villain is Doc Ock all the way.

Hannibal Lecter -- Particularly the one we saw in Silence of the Lambs. Despite not having a whole lot of screen time in the movie, Anthony Hopkins' performance still stands out as being one of the most chilling villains ever to appear on the silver screen.

Darth Vader -- What more needs to be said about the Dark Lord of the Sith? Yeah, the prequels tried their darndest to ruin the character for all time, but he still lives on as one of the all time greats of movie villainy.

The Red Skull -- A lot of the villains on this list have somewhat of a hidden nobility to them such as Doom or Vader. But not the Skull. He's pure evil all the way, and sometimes that's all you need out of your villains.

Clarence Boddicker -- Played by Kurtwood Smith in Robocop. Robocop is one of my favorite movies of all time, and Boddicker is just a great villain with some of the best lines in that movie. "Can you fly, Bobby?" Love him!

Jason Voorhees -- The hockey masked killer from the Friday the 13th films. Not a lot of character development surrounding him over the years, but he's an unstoppable killing machine and one of the best horror villains ever.

Dracula -- The most famous vampire of them all and still a great character, no matter which version you look at be it the original version from Stoker's Novel, the Bela Lugosi version, the Christopher Lee Hammer movie version or several others... well, maybe not the one from Van Helsing, but there have been other great portrayals of him over the years.

My favorite villains are the manipulative masterminds, the guys who are so smart and wealthy that they're practically untouchable and above the law. They're able to evade capture, give the heroes a run for their money every time, and convince the majority of the general public they're "legitimate businessmen" or otherwise upstanding citizens. Plus, they almost always believe they're in the right. And most of them have the resources to do great, heroic things and change the world for the better and upstage their hated heroic rivals, but they're all too petty or mean-spirited to do so.

Norman Osborn (so much more interesting in Warren Ellis' Thunderbolts and Brian Bendis' Dark Avengers/Dark Reign as a rich captain of industry and a scheming, brilliant madman entrusted as America's most powerful and trusted official than he ever was as the Green Goblin.)

Maxwell Lord (makes so much more sense as a villain than a good guy, with his literal power to control minds. Plus he murdered his friend in cold blood: my favorite superhero, the Blue Beetle.)

TAO (an Alan Moore creation from the '90s WildC.A.T.s comics used to great effect by Ed Brubaker in the brilliant Point Blank and Sleeper. Brian, you would love those!)

Grendel (Hunter Rose -- Matt Wagner's assassin/crimelord who is kind of like what Bruce Wayne could have become if he was bored and amoral.)

Ghost (a paranoid, anti-corporate Iron Man villain who was out to kill Tony Stark until Tony told him he lost his company and his fortune, and then Ghost just shrugged and let him go, because he didn't consider him "the enemy" anymore; plus he has a cool costume and great powers, computer hacking and intangibility.)

Deadshot (an amoral mercenary who is the world's greatest marksman -- he claims to not care about anyone and doesn't even care if he lives or dies, but he keeps joining teams, bonding with allies in spite of himself, and proving he isn't a complete heartless bastard. Great costume, too.)

Catman (a former D-list loser who got fat and lost all respect, until he reinvented himself as a charismatic antihero, savage villain, ladies' man, and feared mercenary with a code of honor -- kind of a cross between Batman, Tarzan, and Wolverine -- and also Deadshot's closest friend.)

Captain Cold (pretty much sums up the kind of "working class" villains I've always liked -- guys with a gimmick who consider themselves professionals or thrill-seekers, not because they want to rule the world or murder innocent people for no reason. As the leader of the Rogues, Len Snart inspires loyalty and camaraderie, and doesn't even seem like such an awful person.)

Ben Linus (maybe my favorite TV villain, and definitely my favorite character from LOST. Brilliant and manipulative, I wanted to believe the entire time that he was really the true hero who knew the real answers, and was happy that he got some redemption in the end.)

Wolfram and Hart (okay, maybe THEY'RE my favorite TV villains, from the show Angel. Responsible for all the pain and suffering and misery and corruption and evil in every dimension, they've taken the form of a law firm in our world, and have endless influence and power as a result of their connections. Our heroes never have a chance to beat them, so they eventually attempt to join them and change -- or destroy -- the evil firm from within.)

My list in no particular order

Venom
Carnage
Mr. Sinister
Megatron
Soundwave
Destro
IG-88
Doomsday
Clayface
Trap-Jaw

Darth Vader
Joker
Megatron
Skeletor
Storm Shadow
Mummra
Thanos
The Wicked Witch of the West
Boba Fett
Darkseid

Zoom (Hunter Zolomon) - He wiped Wally West's kids from existence at one point so that's pretty damn villainous, all in the effort to make Flash more of a hero. I think he stepped past Eobard Thawne as #1 Flash villain with that, imo. Kid Zoom was right up there beneath him and had some potential.

Baron Zemo - At his absolute best in the first year of Thunderbolts, he became a kind of anti-villain and has stayed like that up to this point but he's still vastly underrated when put in the big leagues with other Marvel villains.

Hobgoblin - I rather not think about what Slott did to Kingsley but he managed to fool almost everyone in the Marvel universe (and this one) for the longest time. I think there's an excellent chance we can get Kingsley back I just hope it's sooner than later.

Scorpion - Poor, poor Mac Gargan. I believe he was the first Spider-Man villain that I was exposed to watching rernus of the old Spider-Man cartoon on Saturday mornings. I would see him get the ever living crap beat out of him by an insane Spider-Man, continue to be a typical Spider-Man fighting thug, rise up to be almost be a better Venom than Brock (if only Dwayne McDuffie would have been allowed to keep writing him), and now back as the Scorpion. I think, oddly enough, Millar has the best approach with him as he really was the first anti-Spider-Man villain and though I've grown to dislike Millar's work a great deal I still would have liked to have seen him continue with the MK Spider-Man.

Starscream - Constantly on the cusp of ultimate victory but always losing. Sigh. I think what initially interested me in the character was that he openly mocked and revolt against Megatron. I can't remember a time back in the heyday of 80s cartoons where that happened.

David Xanatos - THE MAN. I don't think there was ever a scheme he put into place that didn't benefit him somehow. Runner-up would be Thailog who may have usurped his "father's" place if given more air time plus he had David Keith's voice which is always fantastic.

Vic Mackey - He slithered his way out of almost every predicament he ever encountered and at the very end the cost paid was horrific and showed just how low the man was. It made for extremely compelling television though.

Keyser Soze - If I have to say anything about him then you haven't watched The Usual Suspects.

Walter White - I think he's become an outright villain over the past few seasons of Breaking Bad. You can see why he's done what he's done but it's still smacks of villainy to me. I don't want to say too much about it since everyone might not watch the show. Just like The Shield having him as the main character makes for very compelling television and is absolutely the best television show that's still going, imo.

Rowdy Roddy Piper - I would watch every week as Piper would lose his mind and beat the hell out of people. It was great entertainment to me as a kid. He was always my favorite though I dug Hogan's theme more.

I'm probably forgetting a lot more. These are just the ten that come to my mind at this moment. Although another runner up that I can think of is Deadpool as written by Joe Kelly who kept a blind woman captive and would leave his best friend in his personal torture room. Since he was not always written like that I didn't want to put him up in the list but it really showed a much darker side to the merc with a mouth. It's too bad Nicieza retconned a lot of it causing confusion later on down the line.

My top ten shifts around, but Lex Luthor's usually at the top.

The first Lex Luthor story I can recall reading is Action 544 (I was about eight years old).

It's a really heavy tragedy...

...and it left a permanent impression on me. Not long after, I read Superman 423 and Action 583 (off a spinner rack in a hotel gift shop in Paducah, Kentucky), the last pre-CoIE Superman story (not that I knew that at the time, but still)...

I've always felt really sorry for that particular version of Luthor since, and so he's always been one of my favorite villains.

Post-CoIE, my favorite version of Luthor's the one from Grant Morrison and Frank Quitely's All-Star Superman. Like the Luthor in Action 544, his flaw's that despite his immeasurable intellect, his hatred and jealousy for Superman constantly savagely warps his reason. Issue five, "The Gospel According to Lex Luthor," illustrates this brilliantly, IMHO:

And that version of Luthor's motivation's perfectly simple, too:

1) Adrian Veidt/Ozymandias - REALLY surprised no one's mentioned him yet. C'mon, the guy won!

2) Hannibal Lectur - A psycopath who is not only smarter than you but knows that he's smarter than you.

3) Golgoth (Empire) - Again, he won. Also he was evil enough to do something incredibly dark at great personal sacrafice in the end because he recognized it had to be done.

4) Magneto - I point everyone to Acts of Vengence where Magneto goes after the Red Skull. Great character moment.

5) Doctor Doom - There have been very few times where he was defeated by any hero, typically it is his own hubris.

6) Lex Luthor - Does a reason really need to be given at this point? And I second Jon on pretty much all of his points, especially All-Star Superman.

7) Joker - Once again, no need to get into it

Deathstroke - A more lethal version of Lex Luthor, more willing to see compromise as the answer to a problem.

9) Darth Vader - Redemption is fine and all, but in those first two movies he is absolutely an awesome villain, choking a man to death from miles away.

10) Mr. Burns - All of the above are good pure villains, but none of them are nearly as entertaining as Springfield's power hungry, dog stealing, multi-millionare.

Probably something wrong with me but I generally like a villain more if they have an entertaining personality and aren't just dark, brutal machines. In as I think of them order-

Ming the Merciless-played by Max von Sydow. So powerful that he just didn't give a darn. Did what he wanted. Even tortured his own child when she crossed him. And just darn entertaining to watch, even when I was a kid.

Max from The Losers-totally made the film for me. One of the most amusing villains I'd ever seen but still really evil.

Deadshot-see BBVL-probably my absolute favorite comic book character

Taskmaster-forget whatever continuity rewrite they are doing to him, a villain that can watch you and then kick your butt with your own moves always seemed to be one of the coolest powers ever.

200x Skeletor-there was one episode that really cemented him for me where he totally screws over his minions because they crossed him. It was cool seeing him reborn from a bumbling idiot to that cool scary character that just melts into his throne to plot.

Wrecker-the guy never wins...ever. But he keeps coming back expecting to dominate and then he gets his ass handed to him by Spider Woman.

Lex Luthor-an easy choice but I've liked the guy since Legion of Doom.

Hans Gruber-starts as a cool customer that becomes more and more fun as he gets frustrated

Grocer-Dan Akroyd-Gross Pointe Blank-A ruthless assassin but darn funny guy as well.

Dr. Heinz Doofenschmirtz-possibly my favorite villain of all. He's basically one long villain cliche/metajoke but the writers are clever enough to make that funny in every episode. You know he's not going to win. He knows he's not going to win, but I love the totally elaborate, crazy schemes for generally very little payoff.

Probably not the greatest explanations but I do love watching/reading these guys for a lot of reasons, some not totally explainable.

Glad this is for favorite villains instead of best because some of these guys I'm going to list are pretty bad at what they do, but I sure do love watching them get beat.

G1 Megatron (Transformers) - There are some better accomplished Decepticon leaders, but the original is still my favorite.

Vegeta (Dragon Ball Z) - Now this is evil! Wiping out civilizations, blowing up planets, even eating aliens! Even when he's "good" he goes back to being evil TWICE under different influences and he didn't even fight it the first time.

Cobra Commander (G.I.Joe) - Sure the cartoon version was a little goofy, but the comic version always seemed like an increasing threat. I still remember when he first showed up in the black hood, that just screamed EVIL! Plus he got to work with Megatron a few times.

Darth Vader (Star Wars) - The prequels really hurt his image, but he still remains one of the most intimidating villains to ever exist.

Madara/Tobi (Naruto Shippuden) - A very sly, manipulative mastermind, the secretive leader Akatsuke will step on anyone on his path to take over the world, even going as far as igniting a massive war. And like most great villains he hides behind a mask that only shows his right eye.

Father (Fullmetal Alchemist: Brotherhood) - What starts as a little black ball in a flask finds his end in a power struggle against God Himself (at the hands of humans). It was never about ruling the world, just an endless hunger for power. His behind the scenes control over the government lead to wars and genocide with no redeeming qualities.

The Count/Edmond Dant(bleep)s (Gankutsuou) - From the anime remake of The Count of Monte Cristo, the Count is re-imagined as a man possessed by an evil entity as he enacts revenge on his former friends using their own children to do it. A true gentleman villain, he works from the spotlight rather than the shadows.

Lelouch Lamperouge (Code Geass) - A real tragic villain. He starts as masked hero Zero fighting for the people being oppressed by his own ruling father, but takes on a villain's role when he takes over his father's reign and becomes too powerful. In the end, as a master strategist, he orchestrates his own assassination by his own best friend who has take up the Zero mantel.

Kyubey (Puella Magi Madoka Magica) - Kyubey is proof that you can't judge evil by its looks. What appears to be a typical cute mascot character in this dark magical girl series is actually a heartless creature with no sense of right and wrong and no emotion outside of a perpetual smile and a child-like voice. He selects girls and gives them magical powers in exchange for one wish, the girls then use their powers to fight creatures called witches. He uses the grief that comes from the witch's defeat as a source of power. What he doesn't tell is that the girls will eventually become witches themselves and the circle continues. It doesn't matter to Kyubey if the girls die fighting the witches, he can always get more girls.

Lotor (Voltron) - You have to give the guy credit, he never gave up trying to defeat Voltron. Even though Voltron never really got stronger over the series Lotor just couldn't edge out the Voltron Force no mater what new plan he came up with.

Emerje

Amen! That incarnation of Megatron and the character of Arvin Sloane from "Alias"have to be included on any list I'd put together.

Dr. Doom
The inspiration for my life. My own personal hero.
Read 'Dr. Doom and Doctor Strange: Triumph and Torment'
Dr Doom will do what it takes to accomplish his goals, in this case to free his dead mother from hell, even at the cost of his own soul.
The thing about Doom is that he's correct when he says the world would be a better place with him in charge. We got to see this happen. And Doom is the best example of the honorable villain: he would rather die than break his word.

Dracula
Many great interpretations of this character, as mentioned above. He is a huge part of our culture. As is . . .

Loki
Our best and most fleshed out version of the iconic trickster god. The Joker may actually be the most maniacal and ruthless version of this archetype, but Loki is the real deal.

Godzilla
Like a force of nature that mankind has released upon itself, the Godzilla of the early movies is a far cry from the benevolent beast he later became. King of Monsters and a near-unstoppable force of destruction, the Big G has no equal in sheer devastating power.

Lucifer
The real story of Lucifer is the most powerful and beautiful angel, closest to God, given the difficult task of testing men's faith. It was he who tortured Job at God's request to see if Job would renounce God. Lucifer thought this was unfair and cruel. In his arrogance he thought he could do a better job than God and convinced many of the Angela he was right. His is the most tragic tale of lost grace. And don't bother with the "fictional only" argument. Lucifer had his own brilliant series in Dc comics.

Cthulhu
Even sleeping and imprisoned, dread Cthulhu is a constant source of anxiety for all of mankind without their knowing why. The books by Lovecraft give across this pervasive sense of dread and threat of insanity for simply knowing about him.

Stormbringer
The sentient sword of Elric of Melnibone, Stormbringer lives to eat the souls of all that Elric slays and eventually takes the soul of Elric too. Pure manevolence.

Magneto
It's hard to argue with Magneto's views, because he is most likely right. All we have to do is believe the worst about humanity and his actions not only seem reasonable but necessary. And as mentioned above, Magneto's revenge against the Red Skull at the end if Acts of Vengence was wondrous to behold.

Hobgoblin
This is a personal one for me, because I loved all the old Hobgoblin stories so much. Mix in the odd real-life story of his identity and how he was never Ned Leeds, and you've got something really unique.

Ra's al Ghul
Ra's is right. The world would be better off if managed properly. We rush towards extinction and only someone like Ra's can do what must be done to save us from ourselves, although it pains him do have to do so.