Deus Ex - Most immersive game ever
Marathon - In times of DOOM this game had 640x480, looking up/down and a mind boggling storyline, speech over Ethernet for MP and recording of MP-Games
Beyond Dark Castle - Most favorite platformer of all time
Prince of Persia (mac edition) - Brotherbound got awards for this, 640x480 with 256 colors and lovely details graphics and animations.
Warlords - Best strategy game of all time, easy yet challenging, replay able for years without ever loosing its appeal
Golden Axe - If you knew it, you loved it
Wodan the Trial - Easy to learn, hard to master. AI is not very challenging, but against humans it's splendid
X-Com (1 & 2) - Best squad based strategy of all times (as someone already said)
Gothic 2 - Best RPG ever, perfect mix of arcarde/action and RPG. Good story, interesting characters and detailed handmade world design.
Warrior Kings - Battles - Lots of bugs/imbalances that lead to the most interesting strategies ever seen. Wonderful game mechanics and nice graphics for a strategy game of that time. Very CPU dependent, no Occlusion culling (greatest failure of the engine)
Sins of a Solar Empire - It had to be mentioned!! Perfect game design, give you the feeling to be an overlord of the galaxy
IL - Sturmovik 2 - No Flight Simulator ever came close to this level of realism.
Battlefield 1942 - First FPS to ever allow large maps and vehicle use (so many different types). I've never had that much fun in an FPS before playing the wake island demo.
And many others already mentioned!