Depends. In terms of most widely appealing, Smash Bros Melee, Marvel vs Capcom 2, Street Fighter 2 Turbo, Super SF2 Turbo, and to a lesser extent 3rd Strike are your best bets. There are some tourney worthy KOF games(98, 02, and XI come to mind), and Samurai Shodown 2 is a pretty good one as well, but they're just not as popular. Same with the Alpha games, and the guilty gear games.

Capcom vs SNK 2 takes for-fucking-ever to run a tournament for. I know this from experience. When each game can run about 7 minutes, with a 2 out of 3 games set up for the tourneys, it adds up. The game is pretty boring too in all honesty.

Of course, this is all 2d fighters. Tekken 5 is a pretty damn popular 3d fighter.