Woah, didn't realize this started yet. Good job zeo on doing all of this!
(Note to self: Haven't been on the forums in ages. This is what I get for finally playing Dead Space.)
May be a small list of games, but there are a lot of good ones to choose from. So for those who need a few ideas, then let me offer a few recommendations.
Anachronox
The best game to come from Ion Storm Dallas (not Ion Storm Austin, which have us Deus Ex), this brainchild of Commander Keen designer Tom Hall is one strange beast. It's very much a JRPG, but with a western cyberpunk feel to it. There really is nothing like it, maybe other than the more cRPG Deus Ex. It's quirky, brilliantly written and acted, and highly original.
Duke Nukem 1+2
Before Duke Nukem 3D brought adult humor to the FPS market, a more toned down Duke existed in platformer form. Apogee's new icon brought fun gameplay and referential humor to the genre dominated by games like Keen. It was a standout for Apogee, and it holds up quite well today. Duke Nukem 2 is often seen as the better one, due to it just having a higher production value. So keep that in mind.
System Shock 2
Before the still incredible Bioshock series, as well as the first Dead Space, there was System Shock 2. This was the shining example of a sequel. Remove a lot of the clunkiness from the first, and make the atmosphere even more frightening. The result makes for a deep role-playing experience mixed with one of gaming's most atmospheric settings, along with the return of the ever-menacing SHODAN. This game is an icon of PC gaming, and the GOG version makes it work near flawlessly on modern systems.