SF2 is classic, its the original for me. The old MK games aren't that good, if you ask me. I don't like the new MK games much either. (BTW, who ever posted that mpg of the Ken vs. Chun Li; that was awesome.)
Nowadays, Marvel vs Capcom 2 and Street Fighter Alpha 3 are my favorite for 2d fighters. For 3d,
SSM:B