It's been a very long time since I played any game seriously but Civ IV, so I will have to go back to my top 5 games of all time, not top 5 games I like to play now.
#1 is easy:
The Elder Scrolls III: Morrowind. This game took up most of my gaming time in the years prior to the release of Civ4. Spent so much time on this game playing and also modding. Later I tried Oblivion but hated it. I also have Skyrim, but never fired it up because of fear of what it could do to my work and social life if I happen to like it as much as I liked Morrowind.
The remaining four, listed in no particular order:
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Dune II: Battle for Arrakis. I played a lot of Command and Conquer and also some Starcraft 2. I was thinking about which of those should be included on the list, then I realized it has to be the one that started it all, Dune II. Playing this game when it was first released was something completely different from anything I had experienced before. I can still remember all the details of the game, while the C&C games just mesh into some kind of blur of impressions, where I can't tell which elements are from which game.
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Tie Fighter. X-Wing and Tie Fighter are the only two flight simulators I ever played seriously. Loved them both, Tie Fighter still a bit better than the predecessor. I just watched some youtube review of this game for nostalgia. The reviewer started by saying that you have to have a joystick to play the game. Wrong. I played it through with mouse and keyboard. My arm was so messed up by the constant scrolling.

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Burnout 3: Takedown. Never been much of a racing game fan, but my god this game is awesomeness squared! Crashing cars has never been so much fun. And it comes with several different game modes, all of which are great fun. Twice I played through the game to unlock all the bonuses from scratch. If I fire up the game again, I'm likely to do the same thing a third time.
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Star Control II. I have so many fond memories of this game, yet it now took me quite a while to find out what it was called.
Honorary mentions go to:
-Ultima V: Warriors of Destiny (played it at age 9. Probably never progressed much in the main quest, but loved it anyway.)
-UFO: Enemy Unknown (aka X-COM: UFO Defense)
-Commander Keen series
-Duke Nukem 3D (Only fps that ever got me hooked)
-Sim City series (Not sure which is my favorite, possibly 2000. Didn't play the latest installment.)