For me, it's:
1. Blake Stone: Aliens of Gold. The movement controls are just too dated. If the game was at least as fluid as Wolfenstein 3D in terms of moving your character, then I'd love to play it. But the movement is so choppy that the game isn't worth playing.
2. Robinson's Requiem 1 and 2. Same problem. This game with a better engine, perhaps from the late 1990s or early 2000s, would be much more playable. In it's current state, movement and the UI are just too clunky and dated to be enjoyable. Also, NPC AI is just silly beyond belief.
3. Arma Cold War Assault. This game could have been a blast in it's realism, but the fun is ruined by non nonsensical instructions and storytelling. Many levels lack any kind of instructions on what to do. Also, the opponent AI is terrible, and the bugs can make a level impossible to complete.