I only list '90 games which I actually I played in the '90s (so no Chrono Trigger, Link to the Past or Ocarina of Time as I was a PC only gamer in that decade).
This list differs from my top 50 list I created last year for Smeag's thread, e.g. I took out Day of the Tentacle as 3 of the brilliant LucasArts adventures are already enough for a short list like this, Monkey Island 2 for the same reason and thread rule, Dune II because AoE II was clearly the better game even though I'll always like Dune II a bit more and Civilization (my most favourite game ever) because its successor is also objectively the better game.
So instead of my real '90s top 10 this is a list of '90s PC games which I loved and stood the test of time:
10. System Shock
9. The Settlers II: Veni, Vidi, Vici
8. Baldur's Gate
7. Dungeon Keeper 2
6. Wing Commander Privateer
5. Grim Fandango
4. Age of Empires II: The Age of Kings
3. Indiana Jones and the Fate of Atlantis*
2. The Secret of Monkey Island
1. Sid Meier's (and Brian Reynolds') Civilization II
By the way:
Retrospectively *this is one of the most underrated game of the '90s in my opinion. No site ever mentions it in any top lists (sometimes even not in top graphic adventure game lists). For some reason it's a widely forgotten game unlike Grim Fandango or Monkey Island or the inferior Sam&Max, Full Throttle, Broken Sword. In my opinion Indiana Jones and the Fate of Atlantis is not only a fantastic point&click adventure game but probably the best game based on a movie franchise ever created.