Play as the villain... Because it's fun yo.

Dungeonland you can't spread chaos all over the world but if you manage to get 3 more friends to join you( you will be the dungeon master and they will be the heroes) you will either have fun or... you will never be friends again xD

Civ 5, playing as Ghandi.

Star Wars: Knights of the Old Republic 1 and 2. Both are super awesome and you can decide, whether to be a good boy or a naughty.

Plague inc evolved create a biological weapon to wipe out the planets population

Some Dawn of War series installments let you play as evil factions (not that "good" ones are nice), in particular Winter Assault, Dark Crusade and Retribution. Chaos Rising lets you be naughty too, and your mileage may vary on quality of Soulstorm.
I assume you aren't a nice person in DEFCON either.

Surprised nobody's mentioned Dark Souls yet... :) As you finish the game (depending on which ending you see) you might think hmm, I didn't just kill all the bad guys, I am the bad guy... :)

Also, as an added bonus, if you mumble mumble mumble you can "invade" other players' games to fight them, while they're just minding their business going through the level. Depending on the situation, you will probably end up looking like a real-life bad guy to them...

Skyrim

I want to name a game, but I can't because it would be a spoiler.

Try Portal. In this game you play an evil woman who tries to kill a friendly robot who was only trying to help her.

All GTAs!!! especially with cheatcodes)

DCU Online :P

If you have a PS3 you should ty InFamous, you can decide to be hero or bad guy :D

other than the guys above me said .. i'd say prototype , i felt pretty fucking badass chasing people in the street and cutting them in halfs :D ,

aaah good memories , it've been 4 years already xD

Warioland

Play as the Brotherhood of Nod or the Soviets in the Command and Conquer games

Dungeon Keeper 2.

Dungeon Keeper plays this straight. You're the bad guy, heroes come and try to save their homelands from your evil reign.

The Bard's Tale (2004) you're pretty much SPOILERREDACTED

Overlord, of course.

Prototype places you in the role of the villain, but not objectively. You're more of an incredibly dangerous monster.

Heroes of Might and Magic V - in the Necromancer campaign you're not just a bad guy, but downright evil.

Pay close attention to the things you do for your kingdom in King's Bounty: The Legend. You're a terrible person.

As others says before me: Dungeon Keeper (1 is better than 2 imho), Overlord.
Some classics RPG give you the chance of be really bad ass (Baldur's Gate 1, Mass Effect series, Dragon Age series. Is hard to be bad, but you can do it), dunno Deadpool?, in MK you can play with bad guys and kill everyone XD, Omerta?.

Spec Ops: The Line

Disgaea, although you're more cartoonishly evil than actually evil.
Wizardry IV: The Return of Werdna, where you play the evil wizard Werdna.
Planescape: Torment gives you the option to be really, really evil if you want to.
Monaco: What's Yours Is Mine

relevant

Games where you are allowed to play as the bad guy are sadly rare (though to be honest, I sometimes feel a bit guilty IRL when I commit evil deeds in games, and I guess I'm not the only one, so it's quite understandable). Anyway, here are some good games that lets you play as the bad guy (and not just a not really good person but who in the end ends up doing good. So games like Thief, are out of the picture, and in Overlord you end up doing more good than bad for some strange reason):
Dungeon Keeper. (No way around it, you are evil. You kill, torture & enslave. You can even torture your own minions! 2 is better than 2, but both are good)
Evil Genious (Kinda like DK, but not quite as good)
Planescape: Torment (Allows you to play as a bad guy if you want to. This one is very good in regards to presenting logical moral choices)
Legend of Kyranida 3: Malcolm's Revenge (In the 3rd game, you get to play as the villain, and it's fun!)
Disciples 2 (2 of the campaigns, undead & daemons)
Dawn of War: Winter Assault (one out of the two campaigns. Chaos is pretty evil)

Black and White, Fallout 1 & 2 (child killer perk, enough said), Populous (you can make the population pray to you because of fear or because you're benevolent).

You gotta play Knight of the Old Republic 1. Best RPG of all time and best Star wars game. Even if you don't really enjoy starwars you'll still enjoy the game. You can play as a evil jedi if you wish.