After much thought:
1) Radiohead (though their post-90s career is even arguably better. And this is definitely despite Pablo Honey)
2) Pearl Jam (the thing people forget about Pearl Jam is they were not only considered a better band than Nirvana when Cobain died, but were much more popular.)
3) Smashing Pumpkins (sure, Billy Corgan is a bit of a musical dictator, but he just made great music... until he started Zwan.)
4) Beck (did Beck make a bad album in the 90s? Before you look, the answer is no.)
5) The Flaming Lips (like Beck, didn't make a bad album in the 90s.)
6) Uncle Tupelo (arguably the best alt-country act out there; fans still are pining for a reunion, 15 years after they broke up.)
7) Pavement (Just listen to Crooked Rain, Crooked Rain and you'll see why.)
8) Rage Against the Machine (militantly angry and loud. Some of the best hard rock to come out of the 90s.)
9) Soundgarden (if only for Chris Cornell's brilliant rock voice)
10) Red Hot Chili Peppers (John Frusciante really is a guitar god. Even though Anthony Kiedis is a horrible songwriter, the rest of the group's musicianship brings the band up enough to squeeze into the top 10).