My choices are based on their respective impacts and contributions to the genres as opposed to popularity.

Portishead - trip hop as a genre was defined by this group, a less commercial take then other alt rockers and there live at the Roseland ball room record may be the greatest downtempo/rock/orchestral recording collaboration of all time. A must listen if you like synths and strings.

Failure- I just like them. It seems when conversations come up about nirvana and grunge as a whole this group is strangely absent. Nirvana is exceptional and should replace them on this list but it's my list and I pick failure.

Karate- if you only showed a bunch of highschool kids Midwest emo and steely Dan you would get karate. Nobody knows this band and they fuckin rule. Jazz voicings and voice leading in a rock context. Technically a 2000 record but start with unsolved.

Sneaker pimps- more trip hop but I think sets the stage for what modern alt sounds like today. Groundbreaking and ahead of their time when it comes to arrangement and sound staging. The album bloodsport is irreplaceable.

Cursive- art is hard. A band for bands and as a proud member of team rock viola having a cellist in their group who rips so hard was great. Great lyrics great sound. 10/10 for me. start with the ugly organ.

Neutral milk hotel- I feel like this record speaks for itself in a lot of ways but Jeff mangum is an exceptional song writer and his performance is raw and visceral. I do not believe something like mount Erie or similar projects could exist in a world without him. Aeroplane over the sea is where to start.

Naked city (John Zorn) the next is a jazz artists group who was active in earlier times but these nineties projects are specifically what I am mentioning. Naked city is an ultra juxtaposition of what jazz can should, shouldn't and could be. I have hung out with Wayne horvitz and talked to him about his experience as the organist. It was a wild time a wild project with a wild purpose. If you like jazz and things like ween or Zappa this is a dope group to check out.

A tribe called quest- the amount of hip hop artists and groups that can site a tribe called quest as an influence is so long that the genre would be very different today had they not hit the scene. Low end theory is where I would start.

All my runner ups are: nirvana (oops), diggable planets, bjork (not really a group?), J-dilla, it's not 90s but go listen to madvillainy, dinosaur junior, no doubt, incubus, nerve (JoJo Meyer), green day and my group depth charger! (we're not nineties but if you agreed with my top ten you'd probably dig a few of our tracks)