It is said that every good Hero needs a good villain. On that makes us applaud the Hero for defeating.
I'll start this list with Doctor Octopus. One of the top two Spidey villains, the other one is the green goblin. (Who in my opinion is a bit overrated and Marvel has over-hyped him since the 90s... More on the green douchebag later.)
Doc Ock... What can we say about this pudgy mad scientist with 4 metal arms that would make him useful in the Japanese porn industry? He has beaten Spidey a couple of times. He created the original Sinister Six (Doc Ock, Electro, Vulture, Kraven, Mysterio, Sandman). He almost married Aunt May (To get an Island that she inherited). He killed Gwen Stacy's father, Captain George Stacy... (Ock Started the Trend of Killing Stacy family members, but everyone seems to remember that Goblin killed Gwen...)
Doc Ock even SAVED Spidey's life after figuring out his secret ID while curing him from Vulture's poison. (Of course, the Doc did it in order to kill Spidey himself.) Unfortunately for the insane doctor; Peter's mildly unbalanced clone, Kaine, killed the doctor with his "mark of Kaine"... A super enhanced version of Peter's Wall-crawling skills.
The Doctor was revived in a crazy ritual and now he's back and dying... He tried to take over NY using nanomachines to control all technology, but Spidey stopped him and the emaciated Ock got away.
The next bad guy on my list is one who has suffered from misrepresentation in other media. I am talking about the one man who broke Batman... BANE!!
While this Arkham Asylum video does not make him justice. That guy not only figured out Batman's Secret ID, but he released the inmates from Arkham in order to wear out the Bat. After making Batman wear himself out for months, Bane struck. HE fought Batman in the Batcave and broke the Batman's back. Eventually Bane and Batman do make a truce, but being the one who broke Batman is a huge achievement.
Now for the third villain on this list:
One could argue that Big Boss is or is not a villain. The similarities between Big Boss and Solid Snake are incredible (ignoring the fact that Solid Snake is a clone of Big Boss). In some games Big Boss is a hero, while in others he's a villain. Even in the games that do not feature Big Boss, he still has an influence on the plot. Whether as a liberator or a madman bent on world domination (depends on whose side of the story you hear) Big Boss is still a force to be reckoned with.
Next on the List: Kefka Palazzo...
This is one evil clown. This guy right here makes Sephiroth look like a wimp.
Kefka has no shades of gray, but he is not evil for being evil... He cannot be redeemed, yet there is something that tells you that he is damaged.
He basically destroyed the world and rebuilt it in his image. To him life is meaningless and that the lives of mortal humans are purposeless. So it is his duty to destroy everything.
The backstabbing Decepticon that sounds like Cobra Commander... He's always trying to get rid of his leader, Megatron... Unfortunately for Starscream, not even death can stop Meg... Galvatron from ruling the Decepticons...
Now for the next Bad dude on this list: Keldor + Acid + Extra dimensional being (Demo Man)... I'm talking 'bout Skeletor you fools!
The guy is just awesome and I believe he is the first Villain I knew. I mean he started out as a sort of nice guy that was fighting against racism (but he was banished from Eternos for other stuff aside from being blue...) He meddled in dark arts and tried to burn his own brother's face with Acid. Now after a demo manic fusion Skeletor is trying to enter an old castle, gain ultimate power and rule the universe...