Certainly One Must Fall 2097 is the best DOS only fighter. Its prequel, One Must Fall, should be avoided though, its a bad SF knockoff.
Surprised nobody has mentioned Xenophage and Rise of the Robots! Actually, I'm not. 2 of the worst fighters ever. One you fight with digitized aliens and freaks, and the other you fight with a digitized naked blue man against robots. Horrible, but hilarious in short bursts.
Sango Fighter and its sequel aren't half bad either. And yes, avoid the first SF game on PC. What a load of crap. SFII Turbo was okay though.