#1 RADIOHEAD
They only released three albums in the 1990s but two of them are masterpieces (never mind their debut Pablo Honey.) 1995's The Bends has gone on to inspire many less interesting bands such as Coldplay and 1997's OK Computer is considered by many to be among the greatest albums of all time. On top of that, they were also one of the best bands in the world when it came to putting on a live performance (fortunately, that is still true today.)
#2 THE FLAMING LIPS
The Lips released six albums in the '90s and they were all excellent. They were also extremely varied from 1990's noise rock masterpiece In a Priest Driven Ambulance to 1999's Pet Sounds-ish The Soft Bulletin to 1997's insane experimental four CDs playing all at once freak-out Zaireeka.
What each of their six '90s albums have in common are the following: Creativity, catchy melodies, psychedelic production, unusual lyrics, & interesting song arrangements. Because of that, they are all must hear albums for those who enjoy great inventive music.
#3 THE OLIVIA TREMOR CONTROL
They only released two albums: 1996's Dusk at Cubist Castle & 1999's Black Foliage. But since they are both incredibly epic mind blowing Beatles/Beach Boys inspired psychedelic pop masterpieces I think they belong among the best of the '90s. Memorable melodies, gorgeous harmonies, insane song arrangements, & gloriously dense intended for headphones production: It's all there. These are two of the best albums I've ever heard.
#4 PRIMAL SCREAM
Primal Scream is included at #4 largely because of 1991's Screamadelica & 1997's Vanishing Point. Two brilliant albums that are very different in style. Screamadelica is a great spaced out album which generally represents the "good trip" side of things (although there's a few dark moments too) while Vanishing Point is, for the most part, a much more intense trip. While it missed the deadline for the '90s, I also highly recommend checking out 2000's XTMTNTR which is so intense it makes Vanishing Point sound like Kenny G.
#5 WEEN
Ween is too often dismissed as a "joke band." While their songs can often be quite humorous, they should not be confused with Weird Al. They are a great band both in the studio and in a live setting. I'd recommend starting off with 1997's The Mollusk which is probably more accessable for most people compared to some of their earlier work.
HONORABLE MENTION
Oasis, Nirvana, Spiritualized, Neutral Milk Hotel, Nine Inch Nails, Smashing Pumpkins, The Chemical Brothers, & Blur.