Weezer's Pinkerton album will surely go down as one of the great albums of that decade, and obviously had a huge impact on the music of the past few years (whether thats a good thing or not is up to you).
This will be sacrilege to some, but I think Rage Against The Machine's first album is absolute brilliance, followed by a series of directionless albums that followed the same basic blueprint over and over. Obviously they inspired much of the (very bad) metal of the 90's.
Soundgarden was formed in the 80's and they released several albums prior to the 90's (including their landmark cd Louder Than Love)...I think a lot of their best material went unreleased though. A B-sides collection of them with "Fresh Deadly Roses" and others would be outstanding. However, as much as I love the early stuff. I have a fondness for everything up through Badmotorfinger, but Superunknown is overhyped and not nearly as good as their others.
Again, this is all kind of up in the air without parameters...Black Sabbath released albums in the 90's and they are better than any band anyone will ever mention in any thread, ever, but obviously Sabbath isnt a 90s band. Going by that logic, most of the bands mentioned so far would also not be 90's bands.