To go with the Best Hero Quotes
"I shall command every worm infested son of a ***** that ever died in battle" - Evil Ash - Army of Darkness
"I think I just had an evilgasm" - Xylon - Order of the Stick
"Any line from Machin Shin in the WoT Books"
Karl

"I will kill you, with Death!" -Rictus, (Anachronox).

The Angry Video Game Nerd has a video similar to this, with some quotes, I highly recommend it.
top 10 bad guys
General M. Bison from Street Fighter (1994): "What's the matter? You come to fight a madman, and instead find a god? Do you still refuse to accept my godhood? Keep your God! In fact, now may be a good time to pray to Him! For I beheld Satan as he came down from Heaven!"

The Hammer is my penis. (Captain Hammer - Dr. Horrible (2008))

"They will eventually rise again to face the challenge, but in the meantime... O flowers! O trees! O grass! Come, celebrate my strength! Let the music begin." -Mid Boss, Disgaea -

Apparently Bad Guys are more popular :P
"Evil will always trimuph because good is dumb" - Dark Helmet - Space Balls
"Apology accepted, Captain Needa" - Darth Vader
"Wait a minute. Robin Hood steals money from my pocket, forcing me to hurt the public, and they love him for it?"
[Scribe nods]
"That's it then. Cancel the kitchen scraps for lepers and orphans, no more merciful beheadings, and call off Christmas. " - Sheriff of Nottingham - Prince of Thieves
"I'm going to carve his heart out with a spoon!" - Sheriff of Nottingham - Prince of Thieves
Karl

Darth Traya: "Revan was power. It was like staring into the heart of the Force. Even then, you could see the Jedi he would slay etched on his soul."
More awesome cause she is speaking about you from KOTOR 1.
Kill Bill 1
YUKI: Ferrari...Italian trash. Do you find me hot? Don't laugh! Do you want to f*** me, yes or no?
BUSINESS SUIT: Yes.
YUKI: How bout now, big boy, do you still wish to penetrate me... Or is it I who has penetrated you.

Comment after very rude joke about sending something to everyone at the comppany:
"What can I lose? My Job?" :D
And to turn this to joke: I am working at global Bank :D

"Lets make a deal then, shall we? You cry out for God and I'll stop the moment he arrives." -Count of Monte Cristo
"It's one of those father-son... things." Scar, The Lion King
"F%$k me! They made it!" -Prince of Thieves
"Say goodbye to your two best friends, and I don't mean your pals in the Winnebago." - Darth Helmet