To add:
Fable: RPG
Dungeon Keeper: Older title, but you get to build a dungeon, while trapping and killing all those pesky heroes that try to steal your gold. I seem to recall that in DK2 you can torture them on the rack until they turn evil as well.
Not that it being good or evil had anything to do with how you trained or treated it. A missed oppurunity.
There was an old game for the SNES called “Live-A-Live” that was fan-translated and rom-released. It was unique, because, among other things.
At the end of the mideveal/fantasy scenario, you kill the bad guy, who turns out to be your best friend, and the princess you can to rescue berates you for always being better then him, before she kills himself because you killed her lover(your friend, the bad guy). The main character then becomes the bad guy, the demon king. In the final chapter, you can play the bad guy and, pocess each of the bosses you’ve previously beaten to kill the other 7 heros of the game…or destory the world if you are nearly beaten
Planescape: Torment, of course. The ultimate moral choices in gaming.
Probably not quite what you were looking for, but in one of the Lunar games (the first one, I think–The Silver Star (original Sega CD) or Silver Star Story (PS2)) you get to play as one of the big baddies for awhile (though I don’t think you know he’s a big baddie at the time). Still, he has all his godlike powers and can pretty much kick the poo out of any monsters your party encounters, so he’s kind of fun to have around. Unfortunately you don’t get to keep him with your very long, though.
In Wizardy IV (?) you play Werda (the bad guy in Wizardy I). You also sart at the bottom of the dungeon and work your way up.
Brian
You’re not so much a bad guy in God of War but you’re certainly an anti-hero… Kratos the Spartan is about the baddest badass I can remember in any game. Quite a few innocents fall to your blade and while I felt bad about it, Kratos certainly didn’t…
Chronicles of Riddick: Escape from Butcher’s Bay is another good way to quench your bloodlust. You’re escaping from prison, so your victims are mostly other cons but there are a number of people you can shiv, shoot or otherwise waste that you don’t have to unless you just want to be mean.
EZ
Good ole Tie Fighter. Nothing lifts your spirits like a day of shooting down rebel scum.
To increase the level of Evil in Civ2, add slavery.
It’s easy.
You need a Diplomat unit, a Caravel ship, & some money. Sail to another nation, & locate a Settler/Engineer Unit along the coast. Get your ship next to it, & activate your Diplomat. Bribe the Settler. This constitutes “buying the slaves”. Once purchased, these units cost no food or upkeep money. Immediately put your new Settler onboard the ship. Put the Diplomat back onboard in the same turn, if possible. Or, if a combat unit is nearby, bribe it, too. Fill the ship with units. Sail home, leaving the Diplomat behind, to raise Cain.Set these Settlers to building roads, mining, making fortressses, etc. This works best with civilizations you haven’t had formal contact with yet.
I Was An Atomic Mutant- You play either an invader from dimension x, a giant woman, a giant floating brain, or a generic Godzilla. Smash, kill, eat fleeing civilians.
Looking back to the classics
Aaargh!- Play cyclops, Kong, or Godzilla, destroy villages.
Rampage- Kong, Godzilla, or giant werewolf. Destroy cities. Find hidden bonuses. If your allies run out of energy and revert to human form, eat them.
The Movie Monster Game-Godzilla, giant wasp, giant spider, blob, generic Staypuft Marshmallow Men, giant robot. Pick a city from around the world. Pick a scenario (OTTOMH escape, berserk, lunch, destroy landmark, and rescue).
Manhunter- This was a classic adventure game from Sierra. Aliens had taken over the world and installed a totalitarian government. At one point in the game, you decide whether to keep working for the resistance or become an agent of the aliens.
:eek: I tip my hat, sir!
The most evil I ever managed to do was the “ethnic cleansing” of captured territory—I just tore up and sold off whatever infrastructure hadn’t already been nuked, left enough production capability in the captured cities to produce settler after settler, until I ended up with tiny, depopulated cities that were quickly running out of food.
(The moral of the story: don’t f**k with simuRome unless you want your ass delenda-ested.)
God, that game was addictive.
Personally, I really like Destroy All Humans for PS2 and XBOX. It’s set up to be like an old-style 50’s sci-fi movie, and you’re the alien invader. My favorite weapon in the game is the Anal Probe. Hit the humans with a good charge of that, and their heads explode. :eek:
You get to fly the saucer, too. Loads of fun. Man, now I want to play that. Too bad I loaned it to my friend. 
There was that Jurassic Park game for Genesis that let you play as the humans or the raptors.
In Syndicate you played as a corporate drug-dealer hellbent on world domination. I remember minigunning large numbers of innocent citizens and cops while trying to hit the enemy cyborgs.
Most WWII games with multiplayer allow you to play as the Nazis.
The Hitman franchise.
War of the Monsters. You get to choose from a bunch of b-movie looking critters. It’s fun just running down the street, leaving little bloody splats as you run over people…
Also, Punisher is obviously pretty anti-hero.
The various adaptations of the Romance of the Three Kingdoms games lets you play as Wei, Shu, or Wu, and basically whatever side the character you’re using wins, historical accuracy be damned.
Katamari Damacy’s premise (roll up objects, including people to replace the stars in the sky) is pretty evil. Especially since if you’re just below the threshold to pick something up, you have to ram it first. 
Also, in Disgaea: Hour of Darkness, you’re supposed to be ruling Hell or somesuch, but it’s pretty clear from the plot that you’re the good guys.
That first part makes the FFIV fan in me giggle. Come on, you all know what Kain and Rosa were doing behind Cecil’s back. 
That doesn’t really count though - there wasn’t anything evil about him helping you at the time. The evil part was that he was so much stronger than you when you actually had to fight him as a boss. And don’t get me started on Zophar’s abilities being based on your level in Eternal Blue for the final battle…
As for the OP -
Chrono Trigger, anyone? I wished there was an option to kill Frog and have Magus join your party anyway. I hated Frog with a passion.
I notice there aren’t many console games that let you play as the villain. There are some Wario games, though. Would one count Super Smash Brothers? Come on, we all want to play as Ganondorf at some point.