DOOM, by far. While not the first FPS, it did bring the FPS genre into a completely different dimension and is more responsible for the current style of the run ' n gun side of the FPS genre than any other game.

The original MK was horrible, slow, and clunky. The second was hugely improved (in speed, balance, and just about everything else) but paled in comparison to other popular fighters at the time. The SF incarnations and SamSho 2 were much, much better games. The only things that attracted people to MK were the unique look ("holy shit they look like real people") and the over-the-top gore. As a fighter it is completely overrated.