Baldur's Gate 1 & 2
Planescape: Torment
Neverwinter Nights

These are the games that are the foundation for the other games you mentioned -- aside from Fallout 1 & 2, which I also consider foundation games.

While Fallout 1 & 2 predate it, and are great games in their own right, Baldur's Gate was the game that really popularized the isometric RPG in the late 90s. The first game offers a fair bit of good vs. bad choices (though they're usually more saint vs. selfish jerk than true good vs. evil). The second game, though, kicks it up a notch and does offer the opportunity for some true "evil" moments along with a few moral dilemmas that will challenge even the staunchest paladin.

Planescape: Torment has a similar style (and uses the same game engine as BG) but downplays combat in favor of story, lore, player decisions and consequences of your actions. The game's dialog is top-notch and offers some really touching passages for truly good characters along with some opportunities to be an absolute bastard.

There's also Icewind Dale, which also uses the same game engine as Baldur's Gate and Torment, although it's a much more combat focused game. You can certainly play an evil party, but it doesn't really alter the overall story very much. Good/evil isn't really emphasized much, but if you like the style of Baldur's Gate and Planescape you'll probably enjoy Icewind Dale if nothing more than as a combat-oriented dungeon romp in the same style, with a few hero/jerk moments thrown in on occassion.

And Neverwinter Nights is sort of "meh" on it's own, but it's biggest strength is in the absolutely enormous number of player-created custom adventures available for it -- many of which offer great role-playing opportunities for playing evil or anti-hero characters. You can sort of consider NWN as the "primordial ooze" that Knights of the Old Republic, Dragon Age and Mass Effect evolved out of.