Blood Omen: Legacy of Kain and Legacy of Kain Blood Omen 2 (yes, the title and subtitle have been "switched" at one point). In BO2 Kain's character was unnecessarily simplified (the game was developed by a different team), and I still think it's the worst LoK title, but it should fit into what you are looking for. Other LoK titles don't really meet the criteria, but I recommend them every time I can anyway :P.
From the games that haven't been mentioned yet I would recommend the Suffering and the Suffering: Ties that Bind. Or you can always play Manhunt 1 and 2.
If it doesn't have to be a PC title, then God of War series looks like an obvious choice.
From games available on GOG - besides the ones that other people mentioned there is also Vampire the Masquerade: Redemption.
And on a side note: in Fable: Lost Chapters being evil causes balding :(.

The suffering was good! I ended up being a good guy though. I'd like to see those games DRM free, they had the bad Starforce if I remember correctly.

Deus Ex. "What a shame." Also, killing children.
Sacrifice. Need a bigger army? Murder the villagers and take their souls.

Gothic series. you can steal, pickpocket, kill even the nicest people. You can also screw over people by ratting them out. Just don't get caught or everyone will want you dead.

It's true that those paragon points seem to come in a much greater supply than the renegade ones, but it's not as difficult as you might think. In my current game, I've made it a point to play the renegade role. I have the red eyes (which seem to constantly grow more red) and the heavily scarred face. I've taken and will take the renegade path on pretty much every mission. You might think that playing a renegade character will automatically cost you friendship points with your crew, but that's not always the case. In fact, they actually like the renegade responses you give them many times, because the renegade answers are often more tough than mean. Of course, there are times when a renegade response directed at a crew member isn't kind, so you may want to use the neutral response instead. In other words, you don't have to use paragon responses to get your crew to like you. Just be aware of what the potential answers are and how they fit into the context of the situation.

Dark Messiah: Might And Magic (evil is, in fact, encouraged. Why are you called the DARK messiah?)
Any Elder Scrolls game.
Overlord series
Disciples series (at least some factions are explicitly evil, and all are genocidal)
Dawn of War series (every side is sociopathic, but special mention goes to Chaos, who will destroy everything in the name of their dark gods, and the Orks, who will destroy everything because it's fun).
The Deus Ex series (moreso in the second game than the first)
Arx Fatalis (kinda: you're basically permitted to almost everyone and still finish the game)
Neverwinter Nights (up to a point: "Evil" usually means "Jackass," at least in the first game. Expansions are better.)
Destroy All Humans (cruel destruction is the entire point).

I had a perfectly legal copy of the Suffering DRM-free (I still need to unlock the neutral ending). The sequel was StarForce-infected, and that was the main reason why I didn't buy it. I had a chance to play it for about an hour however (and saw the rest on YouTube). I'm usually against celebrities in games, but Michael Clarke Duncan made a really great performance.
I still need to buy the re-released version (hopefully it doesn't have SF in it, and if it does... well, there are ways around that :P). They still sell it here for a really low price.
While I really like Dark Messiah, that game doesn't really give you any freedom in the moral choices department. You have 4 moral choices in the entire game - all near the end and all affecting the lives of 2 persons. There is no real way to play the entire game as a a mean SOB.

There's a neutral ending? Now I definitely need to play that again. I thought there were only two endings. Seems that Midway own it... but aren't they bankrupt? Who does it belong to now?

There is a game on here called "Evil Genius"
Sort of like dungeon keeper but with a 60s spy theme.
Oh, and if you have Neverwinter Nights, there are some really good evil mods, like A Hunt in the Dark