I noted that the topic was albums of the 90's, not just albums from "90's bands" so....
5) Tori Amos - Little Earthquakes (Set the stage for female artists of the 90's and one of the best track-for-track albums of all time, even though calling it "rock" IS a bit of stretch here. But, I'm Dave, so it counts)
4) The Flys - Holiday Man (One of THE most underrated acts of the 90's. EVERY track on this album is a fave of mine. They had a unique sound in a time of endless clones, and it is too bad they only lasted two albums. Seriously, if you can get this album, get it.)
3) Phish - A Picture of Nectar (Phish epitomized the 90's for me...especially since I was dragged kicking and screaming into the decade. Living around Vermont at the time Phish became popular, I remember seeing them as a bar band at the very club (Nectar's) that bore the album's name.)
2) Phish - Rift (Arguably the best Phish album of original material. I miss Phish.)
1) Rush - Counterparts (This album saw Rush ditch the over-synthed albums of the 80's (which I DID like), and out-grunge the grunge movement. They did it by returning to dirty sound, but with a couple decades of expertise in songwriting. Songs like "Stick It Out", "Animate" and "Cut To The Chase" are those kinds of tunes that bands like Pearl Jam wished they'd written.)