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10. Nethack. After decades it's still the best dungeon crawler.
9. Grim Fandango. I had to include at least one classic LucasArts adventure game here, and Grim Fandango has the best soundtrack, the best style, the best story, and so many of the best characters.
8. Portal. The only flaw in this game is that it was too short, and it paved the way for so many other brilliant first-person puzzlers like The Talos Principle, The Turing Test, Tri, Q.U.B.E, Qbeh-1, and so on.
7. TIE Fighter. I almsot put X-Wing here because it was my first fully 3D game and so mindblowing for its time, but TIE Fighter was even better.
6. X-Com UFO Defense. I almost wanted to put X-Com Apocalypse here, I like the style and the feel of Apocalypse even better but it also has a lot of flaws while UFO Defense is flawless (except for the bug where the difficulty was always beginner, but that's been fixed for a long time).
5. Half-Life. Not just for the main game, which is great, but for all the mods like Team Fortress Classic, Counter-Strike, Day of Defeat, Natural Selection, and I feel like I'm forgetting a few others. And also for the way it encouraged and popularized that kind of modding.
4. Star Control II. The soundtrack, the dialogue, the story, all the alien species, and the gameplay all come together to make this the best space adventure. The games Starflight I and II also deserve honorable mentions here for being obvious inspirations and two of the best games of their time, but Star Control II took the concept and turned it into a game that's even better in every way.
3. Morrowind. The otherworldly atmosphere, the lore, and the story make Morrowind the best Elder Scrolls game. The leveling system had its flaws, but there are mods for that.
2. Sid Meier's Alpha Centauri. The tech tree, the wonders, the customizable units, the ideological factions, Planet, and the whole feel of the game make this still the best one in the Civilization series.
1. DOOM. Maybe a mainstream answer, but that's because it's true. The soundtrack, the style, and the gameplay were all perfect and revolutionary.