Sims:
- TIE Fighter (<- awesome, if you're into Star Wars and despise the Rebels)
- X-Wing (Both of them are included in the X-Wing Trilogy AFAIK, along with X-Wing Alliance)
- Jane's 688(i)
- Jane's F/A-18
- Red Storm Rising (1989, so really old, but still good)
- Flying Corps Gold
- Aces Of The Deep
TBS:
- Master of Magic (<- awesome)
- Master of Orion (both I and II, I prefer the latter)
- Battle Isle 2
- Panzer General
- History Line 1914-1918 aka The Great War (awkward controls though)
FPS:
- Shadow Warrior (same engine & style as Duke3D; be sure to check the enhancement mods for recent graphics cards)
- DOOM I,II, Heretic (<-awesome), HeXeN. They've been mentioned before, just wanted to say that there's a great
source port for these games.
Point and Click Adventures:
- Beneath A Steel Sky
- Kyrandia series
- Indiana Jones series
- Monkey Island series
- Toonstruck
You could also check out
Liberated Games.
Mobygames hosts a great search engine.