Well, there's Wario, obviously.

The Dragon Quest Slime (which started out as a random monster) now has a couple handheld games to its credit.

Does Dr. Robotnik's Mean Bean Machine count? I think it should! Throw Shadow the Hedgehog in there, while you're at it.

Big Boss has now had a starring role in two MGS games.

Slight spoiler, but what about Soma in CV: Aria of Sorrow?

grobda tank.

OK, dessgeega wins obscurity of the millenium award (it's a Xevious spinoff):

http://en.wikipedia.org/wiki/Grobda

Grobda is available on GameTap, actually!

What about Kid Dracula? Does he count? (pun intended)

if so you'd have to include castlevania III and Symphony of the Night which both have alucard as a playable character.

If you were to allow that then maybe you'd have to allow Advanced Guardian Heroes because everyone enemy in the game is unlockable as a playable character?

Speaking of Advanced Guardian Heroes, what about games where the hero of the first game is the villain of the previous one? Lufia II kind of does something like that if I recall. Also maybe Neo Contra?

In conclusion I have nothing to contribute to this other than weak puns and idle speculation!

Was Wario in a game before Wario World?

Yeah, he was the villain of Mario Land 2 for the gameboy.

The Legacy of Kain series. I could never remember who was supposed to actually be the good guys after a while. I mean, technically Blood Omen 2 had you playing as a very evil Kain, but he was the bad guy in the Soul Reaver games and then good again or something in Defiance...and...it's been too long and is too complicated to remember.

And what about Donkey Kong Country? Seems like one of the biggest ones to me.

D! K!
Donkey Kong!
D! K!
Donkey Kong is here!

I don't think Shadow or Alucard count, since they started in protagonist roles. Even if they're both bosses in their starting games.

Mega Man's Bass ended up in a starring role, so did Mega Man X's Vile. But the coolest starring villain of all has to be Tron Bonne!

Um... Metaknight.

It's not quite the same, but the Street Fighter Alpha and Street Fighter 3 games both included characters that were originally enemies in the Final Fight series. Looks like Capcom likes to shake things up a bit.

I think the most notable one for me was 'Malcolm' in The Legend of Kyrandia III: Malcolm's Revenge. I always thought Malcolm was the coolest villain in the original Kyrandia game, a clever jester with a sharp wit and penchant to harm things for fun... so when Westwood released the third game with Malcolm as the player character, it was a totally cool concept. Shame the gameplay was a little -too- nonlinear, though...

Also on the 'not quite the same' note, you played as the villain in Dungeon Keeper, trying to stop the cliche game 'heroes' from conquering the dungeon.

It's also interesting that the 'villains as main characters in spinoffs' thing is popping up outside of games, too. For example, the musical 'Wicked' is a prequel to the Wizard of Oz, with the Wicked Witch of the West as the starring role.

Mario himself was the villain of Donkey Kong Jr.

Of course, Smash Bros. Melee had Ganondorf as playable.

Robotnik/Eggman has gradually transitioned from being a villain to playable in the Sonic Adventure games.

In the world of licensed games, the previous Jaws games , such as Jaws for the NES pitted humans against the shark. Then Jaws Unleashed let you play exclusively as the shark.

how about "a TIE Fighter pilot?"

It would be interesting, from here on perhaps, to note whether the villain remains evil in his/her spinoff, or the character adopts a noble cause or whose actions are made understandable through character development.

Nobunaga is the enemy in lots of traditional japanese history games, but you can play as him in sengoku basara and others.

Mecha Sonic counts, sort of, though he didn't have his own game.

Rampage almost counts - not original characters though.

Here's a definite: Allen's Battle Chronicle. Cellphone Metal Slug sidestory in which you play as the bald guy with the huge gun.
see here: http://game.snkplaymore.co.jp/mobile/i-mode/special/allen1.php

Knuckles pretty much had his own kind of cartridge invented for him after Sonic 3, and Black Bomberman was the bad guy in the earliest bomberman titles. You can play as two Xen Aliens in the PS2 version of Half Life if you complete certain things to the game's satisfaction, and that's ignoring the blatantly obvious Opposing Force for PC. Yuri's Revenge let you play as Yuri in Red Alert 2 multiplayer, and um... Street Fighter Champion Edition let you play as the bosses?

Oh! And there's a Gradius game where you play as one of the boss ships!

Isn't it debatable wether or not Knuckles was a bad guy? And Shadow wasn't in the very first STH game, was he? (just asking) Plus I don't think Eggman counts, since he doesn't technicaly have his OWN game.
-wii out