Best Bad Guy!

[Cosmic Humor]

Since you didn't limit us to video games, I'm going to have to go with Professor James Moriarty from Sherlock Holmes. Honestly, without him the supervillain would never have truly evolved. Even besides that, he portrays the epitome of the clever and brilliant bastard that can beat the hero at his own game.

 

[dududf]

Atlas, from Bioshock.

I liked that guy, he's one smooth criminal.

 

[Eclectic Dreck]

SHODAN, closely followed by The Purple Tentacle.

 

[Julianking93]

Kira, Liquid, Ganon, The Emperor, The Templars, Sephiroth, the computer chick from System Shock 2, Mion (Shion?), Mariko, Vicious, and Akira.

If you can name where all of those villains are from then you are just as nerdy as me.

Sounds like a challenge:
Kira: Death Note
Liquid: Metal Gear Solid
Ganon: Zelda
Emperor: Final Fantasy 2
Templar: (Hm) Assassin's creed?
Sephiroth: Final Fantasy 7
Computer chick from System Shock 2: System Shock 2 (haha)
Mion (Shion?): I dunno (the only Shion I know is from Xenosaga)
Mariko; Elfen lied?
Vicious: Cowboy Beebop
Akira: Akira

I think I'm close...

Close.

Kira, yes
Liquid, yes
Ganon, yes
Emperor, no. Emperor Palpatein from Star Wars
Templar, yes
Sephiroth, yes
System shock 2, yes
Mion (Shion), no. Higurashi. Look up top 11 anime villains from The Dude in Suede.
Mariko, yes. First one to get it right
Akira, yes
Vicious, yes

 

[dalek sec]

Megatron from Beast Wars.
The Daleks from Doctor Who.
John Cavil from Battlestar Galactica.
The Ori from Stargate SG-1.

 

[ramzaw]

Best villain ever? Two-Face. However, I have never wanted him to best batman.

The villain I wanted to best the hero? He's not my favorite at all, but Voldemort. I wish he'd blown up Harry.

 

[malestrithe]

Dahlia Gillespie. She was the reason for the craziness in the original Silent Hill.

Bob the Goldfish.

Mike Tyson. Even if you remember his pattern, he still kicks your ass.

Goro. Still the best claymation villain in the Mortal Kombat universe.

 

[metacree]

Freiza, best villan ever.

 

[Stevanchez]

Darth Vader and Tyler Durden(Not really sure that counts because he was technically the protagonist also)

 

[theodin77]

Luca Blight
The only video game villian that I know of where the hero just wasn't strong enough to kill him.
Cloud has owned Sephiroth many a time, but it took a freaking army and then some to kill this SOB.