This one is really tough.
Between Ultima Underworld, whose influence is to be found in plethora of genres, Ultima VII, which is even today superior in many aspects to modern RPGs, Wolfenstein 3D that was the first FPS as we know them today, Alone in the Dark which was template for later survival horrors like RE and SH, and Dune II, which set template for RTS games.
Then there's pure fun games like Mario Kart, Mortal Kombat, Virtua Racing, Lost Vikings and Comanche: Maximum Overkill (I knew people who were buying PC for that due to its, for the time, mind blowing gfx).
Ultimately (pun intended), I have to go with Ultima (either one)...and since Underworld is in the poll, that will be my vote.
Honorable mention to Indiana Jones and the Fate of Atlantis, to this day one of the best point&click adventure games and Darklands, very ambitious open world RPG set in medieval Europe which is considered granddaddy of real time with pause combat in later Bioware's RPGs, as well as being one of the influences on Elder Scrolls (along Ultima... of course).