90's was in my honest opinion one of the hugest times for underground music. Fuck all that mainstream crap, with the exception of some grunge it was all about the underground. Metallica/Slayer/every good metal band of the 80's went to the shitter come 1991.
Alternative grew it's wings in the late 80's and early 90's with bands like Sonic Youth and My Bloody Valentine (and earlier on The Pixies) encouraging experimentation in music. Pushing the boundary of what was actually considered music. These were the roots for those cool indie bands you see today. The Mars Volta learned a lot form Sonic Youth. As Rads can attest, an album like "Loveless" is absolutley beautiful sounding, yet is only the sound of a guitar on 11. Later on in the decade we have those other awsome alternative bands such as Radiohead, Incubus, etc...
Radiohead - Paranoid Android;
Sonic Youth- 100% (Not 90's but listen to Teenage Riot by SY)
My Bloody Valentine - Only Shallow, SoonerOn the heavier side of alternative, we branch out to bands such as Rage Against the Machine, Tool, Faith No More, RHCP (pre-Californication), and The Deftones. (imo, I don't consider that mainstream). All 3 of these bands still having a long lasting effect today.
Alternative hard rock also began to include hip-hop into their music. I'm indifferent on this subject. Limp Bizkit is very much a no, while newer bands such as Flobots, and the Transplants do it alot better.
Tool - Stinkfist"""""
Deftones - Change"""
Faith No More - Epic""""
RATM - Know Your EnemyI am a fan of Nirvana, Soundgarden, Alice in Chains and that whole scene, but what is important to understand is that it is not grunge that was important, but the massive roots it left behind.
Alice In Chains - RoosterThe Day I Tried to Live - Soundgarden"""
All Apologies/Serve the Servant - NirvanaSeattle and the Northwest was a huge explosion of groove/stoner metal. Sleep's "Holy Mountain" is one of the iconic albums of stoner metal form 1993, this led to band like Electric Wizard, while their later drone metal albums are still considered benchmarks (63 minute songs for example). Curt Cobain alone had a huge part on the stoner scene. His roommate (and the man who bought his shotgun), Dylan Carlson, formed a band called Earth which are widely considered the godfathers of drone. Cobain even auditioned to play for The Melvins. Without these bands we wouldn't have BORIS or Sunn 0)), or any form of ambient rock.
Sleep - DragonautThe Melvins alone are worthy of their own heading. Any metal/hard rock band today cites them as an influence, yet they are still just a wierd psychadellic rock band from seattle.
In the southwest, and texas, people started combining sythesizers with heavy electric guitars to creat industrial, and probably the evolution in goth from The Cult to KMFDM . To this we can thank them for Ministry, Fear Factory, Skinny Puppy, Prodigy, once again KMFDM, and any electro-rock band you can think of.
Ministry - Jesus Built My HotrodIn Europe and the Eastern USA, extreme metal took a whole different turn. Thanks to bands such as Death, Morbid Angel, and Possessed metal was becoming faster, eviler, and more inrticate. Death created several amazing albums in the early 90's such as "Symbolic" and "The Sound of Perseverance." Death metal exploded. British band Carcass had a triple hitter with "Necroticism", "Heartwork", and "Swansong," emerging along with In Flames as the kings of Melodic Death. Brutal Death grew with bands such as Cannibal Corpse, Nile, and Suffocation all debuting in the 90's. Any of you metalcore/deathcore kids out there who like KSE, Chimera, Lamb of God, Job For a Cowboy, or Atreyu (etc...); this is your history.
Carcass - HeartworkIn Northern Europe, paganism and satanic rituals were becomming ever more popular. Black Metal, a simpler, more orchestral form of old school death metal grew out of this. I like to refer to it as "European Hardcore." The musicians weren't very good and the production is terrible. It was like the Norwegain version of LA hardcore suburbs circa 1980. This era was more about attitude and actions than music, and suicide, church burnings, and murder ws a common element of the scene.
Dimmu Borgir - Mourning PalaceBlack Metal and European Death metal has since evolved into a legitimate genre, adn satanism is now just part of the act, and is not as serious. Check out Dimmu Borgir; they are the prime example of good black metal.European death metal took off closer to the 00s, borrowed alot form Carcass and the American scene.
Meshuggah - New Millenium Cyanide Christ - Deliverance
Dance and Electronic music evolved form guys with stupid haircuts to the club/rave scene scene. Daft Punk is a good example of the music that out grew Flock of Seagulls...... I dont know to much about this scene, but I know it was the 90's ditched New Wave for this.

Modern club, electronic and dance is the main product of ths evolution.
Daft Punk - Da FunkPunk died and Hardore was abandonned. To this we now have Pop Punk, Ska Punk, and all those other hated versions of punk. Curse or Blessing? Swedish Hardore was it's last breath. Refused made an attempt to change it with 'The Shape of Punk to Come..." (Hands down on of the best punk albums ever), but lost to Greenday and Blink 182. Refused's influence can still be seen in alot of that new stuff that they call hardcore. Underoath, From First to Last, screamo? "
New Noise - Refused" "
Blink 182 - Dammit -
Rancid - Time BombJazz abandonned synthisizers and turtlenecks for actual instruments.

Virtuoso music got better. Steve Vai's "Passion and Warfare" album is all the proof you need. "
The Audience is Listening -Steve Vai"
Gangsta Rap. P Diddy, NWA, Biggy, Tupac ,yaddah yaddah "
Straight out of Compton - NWA"I'm probably forgetting a whole lot, buut it's late, so if I come up with anymore I might add it. Now you know what I do when I'm not playing TF2
Uggh, this is such an incomplete history of a great musical decade.
PS. A fter reading this over, it;s kind of cool to see how much of this actually did have moments where it did tie back to mainstream, directly or indirectly.