Half-Life. Obvious, really.
Master of Orion II. Perfected the space 4X genre and has never been bettered (although it did have some micromanagement issues, admittedly).
Freespace (1/2). Brilliant space dogfighting combat, with just enough story to keep it interesting without getting in the way of pure action.
Thief (1, especially 2, and to a lesser extent 3). Best games ever. Involving storyline; rich, immersive world; unique gameplay; quirky dark humour; great replayability with extra objectives on harder difficulty levels… One of the few series of games I’d rate on the same level as the HL series.
Myst (1 thru 4, 5 was a bit pants). Really nice, detailed stories; clever logical puzzles; gorgeous audio and visuals, even back in 1994. Can’t fault a game that spurred adoption of an entire storage format.
That’s all I can think of off the top of my head. There are doubtless more.