CRITERIA
You are not limited to just one game. List as many as you can, with the following caveat:
It must have adequate playability even today.
Theoretically, Railroad Tycoon by Microprose is a great game; but today, it just plays like total ass, due to primitive graphics, wonky control scheme, etc.
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My submissions:
Doom 1 and 2 for PC
Admit it; you still like to play E1M1 on a emulator and have memorized IDKFA and IDDQD into muscle memory. Even today it doesn't look that bad. It's certainly aged a lot better than Wolfenstein 3D and the numerous FPS shooters released around that time, like BLAKE STONE.
Mutant League Hockey for Genesis
Mutant League Football wasn't that great, but MLH far exceeded it's precedessor, being a lot more playable as a beer and pretzel game due to the mechanics of hockey (near continuous action), and the graphics are good enough for the time. The control scheme's easy to pick up, and there's nothing like winning the Mutant League championship because you've killed all the other teams in the league, forcing them to forfeit every game to you.

Pirates! Gold for Genesis
The best version of all the original Pirates! games. Basically took the awesome graphics of the Amiga version and implemented them in a much easier to play format.
X-COM UFO Defense/X-COM Terror From The Deep for PC
Let's not kid ourselves, TFTD is basically a mod of UFO; with the difficulty dialed up quite a bit. Still, the graphics and control scheme for both games work fifteen years later.
Civilization 2 for PC
This is in my opinion, the best version of Civilization -- it was far more playable than it's precedessor; and had game mechanics which still haven't been equalled by any of it's later successors -- I've only gone up to Civ 3; that was enough for me to swear off any future Civs -- spearmen sinking battleships my ass, along with the retarded border/culture system as well as the "need resources" which was implemented poorly.
Master of Orion 1/2
Whether you like 1 or 2 better is a matter of personal taste. I tend to gravitate towards MOO2, because the game was improved a lot regarding controls and graphics over MOO1. Let us not speak of MOO3.