Yeah, this is an old topic ressurrected, but I have a similar answer.
One of my favorites still goes to the world's first Super in a fighting game.
Ryo Sakazaki's famous original Desperation move. It's still alive, and kicking (as well as punching).
Also, one of my other favorites also goes to a Sakazaki. Yuri Sakazaki's Uppercut super (the one that pays homage to Ryu's Street Fighter 3 one). However, I will mention the year as well. KOF '99. (Or 99' Evo for the home users). Why? Because it has the best audio in any super I've ever heard. That 2nd hit of that super can almost bust Sub-woofers, it's that good. Probably the heaviest hit I've ever *heard* in any fighting game, to this date. Yuri's super doesn't only sound like it hurts, it sounds like she plain demolished someone's insides with that hit.