TFX- Because it was a fantastic flight sim, with a killer soundtrack
Descent Freespace- For all the reasons BlackVertigo mentioned
Link: The Faces of Evil- ...
Warhammer 40,000 Chaos Gate- Because it may just be the hardest game I have ever played. Or I sucked when I was younger.
Star Wars X-Wing Alliance- Because it may just be my favourite game. Ever.
And, with only it's predecessor being mentioned,
Star Wars Dark Forces 2 : Jedi Knight- Because of the-
-Enourmous, well made 3-part levels, which had fantastic scale for it's time
-Ingenuity inherent in the level design (Oh, there was this one fantastic level in a cargo ship, err, I'd better get on with this)
-Great graphics and effects (FOR ITS TIME)
-Intelligent AI that could scare the crap out of you by leaping from behind a crate and beating you to a pulp
-Fantastic integration of FPS with puzzles built into the levels
-A variation of excellent and interesting weapons
-First/third person lightsaber. Come on, that should be reason enough
-The ability to choose your ending from your actions and reflection of that path in cinematics, levels, and your character's abilities
-Full Motion Acted cinematics (Well I liked them)
-Having about 30-odd force powers to torture the innocent and the not-so innocent with (lightning! Firey death Ball! Choke! Throw people at stuff! DEATH EYE BEAMS [Seriously, no joke] and all sorts of stuff)
-Excellent soundtrack and fantastic atmosphere.
And a host of others which I can't be bothered to talk about. But I'll give mention to a few I can think of.
C&C 1
C&C Red alert
C&C Tiberian Sun (if that is pre-Y2K)
And how did I almost forget, MDK, for being the wackiest and most excellent third person shooter I have ever played.