Pumpkin-Head

Believe me, I was also asking that question. Dinosaur Jr., aside from being influential upon numerous rock legends (Kurt Cobain for one) also boasts J. Mascis, who is perhaps the best guitarist/songwriter of the entire 80's and 90's. Yet, no mention of them whatsoever. But then again, you have to keep in mind that this is an MTV poll, and as such, respected groups like U2 and Depeche Mode are placed next to NSync, etc...
I have to also go with Radiohead, although I just about nearly picked The Smashing Pumpkins. For one, Billy Corgan was far more reaching in the mid-90's then any of these teen groups today. However, Radiohead won out because (a) Like Gabe said, they're current, and they'll be around for a while. (2) Billy Corgan has admitted to Radiohead being one of his personal favorites in past interviews. So naturally I figured that there'd be no hard feelings...heh heh.