Only listing the ones I had and have played:

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Abuse - still available and playable on Linux

Alone in the Dark - friggin awesome

Battle Chess - I bought this when working at Radio Shack

BioForge - one of the best games I've ever played. There was supposed to be a follow up, never saw one ever planned or rumored.

Blood - Played while going to training at Novell for NetWare, it used IPX networking for multiplayer

Carmageddon - #2 also. Very unique game and was very cool

Commander Keen - Not as memorable as I would have thought. Good though.

Crusader: No Remorse - Also Crusader: Redeemer - awesome playables time and time again

Descent and Descent II - first 6 axis game that worked well and friggin rocked. I memorized all the levels. There were a few repeated patterns in fighting... but very well done.

DOOM & DOOM II: Hell on Earth - Of course, everyone played this. Both available in Linux

Duke Nukem 3D - Had about 400 different mods for it as well. different modes of play and just friggin full of awesome.

Full Throttle - Had the box, until 2 years ago when I cleaned. It was so cool looking and fun to play.

Grand Theft Auto - The original was fun to play and was a looking down driving game with a lot of great play and re-play.

Heretic and Hexen: Beyond Heretic - Played these for freakin hours... love some of the special powers that were self hurting... haha!

LSLITLOTLL - Loved the censored seen bit... funny game also.

Mechwarrior and Mechwarrior II - way to much time wasted on these games

Nethack - still being developed and working. Its crazy.

Out of this World / Another World - I still have the decode disk/ring for this one.

Quake (and Quake II) - Played to many hours. QII played in DOS with reduced resolution. QII available in Linux

Red Baron - Changed what I though about flight/airplane based games.

Sam and Max hit the road - Pretty good humor and funny resolutions for the game and mini games.

Star Control II - Still play it from time to time.

Starflight - Still attempt to play it and win... still haven't yet.

Syndicate/syndicate Ware - Started a whole new genre. Wow.

System Shock - The Game upon which ALL other FirstPerson/Immersive/task oriented games are measured. Still IMO never has been matched.

The Dig - Got the book with the first release... meh. Game was better than the book. I couldn't read the book.

The Incredible Machine - Started everyone's interested in very overly complex machines.

Secret of Monkey Island and MI:2 - More awesome

Ultima Underworld: The Stygian Abyss and Labyrinth of Worlds - Shut the eff up. Very detailed and FUN. I miss these games similar to these.

Wing Commander I-IV and Privateer - Great play... over and over.
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Wasted way to much time on these and this post.