There are so many good games from '93, it is hard to not feel bad for having to vote for just one. Especially when, at least for me, it comes down to really only dilemma from that year, Myst or Doom, given how much both games changed how people think of games. But ultimately, no matter how great Doom was, and better than Wolfenstein 3D that started FPS genre as we know it, I have to go with Myst, for it was THE game that changed adventure games and gave birth to very distinct first person puzzle adventure subgenre.
Other games that stood out from that year for me were Link's Awakening, Settlers, Syndicate, Master of Orion, Frontier: Elite II, Betrayal at Krondor and Star Wars: X-Wing. (and of course crapload of great P&C adventure games, '93 was full of them)