In no particular order (all of these are legendary in their own right)
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Tyrian 2000
Most detailed game of its type, with the most options, secrets, difficulty choices, etc. Also features a unique "loopback" where once you finish the last level, the game loops back to the first one instead of ending. Last time I checked, Tyrian 2000 is either public domain or open source, and it's freely available on GOG. Go play it now - if you have time and haven't played it, you have no excuse not to.
Newer games of the same type have better graphics, but as far as actual customization and strategic depth are concerned, none of the newer games have anywhere near as much.
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Inner Space
If anyone else has played it or even heard of it, I would be surprised. It's supposedly the only games that has been played in the same way from the original Windows 3.x until today.
Wide variety of spaceships and items. Randomly generated waves/missions. Incredible detail and visual effects for its time. Amazing considering it was written in the early 1990's.
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Might and Magic VII
The pinnacle of a legendary series, probably better than the rest of the series combined. Single-player, multi-character real time combat, with a turn-based option. Superior game design, balancing, variety of NPCs. Original storyline with 2 paths for replayability. I also challenge you to find any game that makes 640x480 2D sprites look more detailed. As far as I know, there are no other games made in its style besides Might and Magic 6 and 8.
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Elder Scrolls IV: Oblivion
A lot of you are probably going to question why I didn't pick Morrowind (best storyline in an Elder Scrolls game) or Skyrim (for the better game engine). The main reason is that Elder Scrolls IV: Oblivion was the last game in the series with a disc-only option for PC, and it actually had a functional scripting engine unlike Morrowind. (Skyrim is only available on Steam for PC games. Moral of the story for developers/publishers: mandatory DRM and discrimination against PC gamers = miss out on awards)
NOTE: If you are planning on getting the disc edition of Elder Scrolls Oblivion, avoid the "Game of the Year" edition (specifically, avoid the Shivering Isle expansion) - I read somewhere that it comes with some DRMs that can damage your computer. As far as I know, the base game has only a disc check as DRM (must have the disc in a DVD reader to run the game).
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Jazz Jackrabbit
Combat-oriented platformer - unlike most other platformers that attempted to imitate Nintendo's Mario franchise, Jazz Jackrabbit was about fighting turtles instead of difficult jumps and maneuvers. It also had a sequel that supported splitscreen multiplayer.