I know some of you may not consider some of these labels as "indies".
However, I have my reasons for each one, so there.
It's just a partial listing of the artists, obviously. (and of labels)

4AD Records Bauhaus, His Name Is Alive, Pixies
Alternative Tentacles Lard, Jello Biafra
American Recordings Skinny Puppy, Timmy!
Aquarius Records Corey Hart
Astralwerks Chemical Brothers
Beggars Banquet Bauhaus
Caroline Lords of Acid, Smashing Pumpkins
Dreamworks Records Eels, Elliott Smith
Firstworld Music Bill Rieflin, Jeff Greinke, Hana, Land, Radio Chongching
Interscope Records Dr. Dre, Primus
Invisible Records Pigface, The Love Interest
Jetset Records Prolapse
Killrockstars Elliott Smith
Massproduktion Garmarna
Mute Records Cabaret Voltaire
Nettwerk Skinny Puppy
Nothing Records Nine Inch Nails, Marilyn Manson
Subpop Nirvana, Reverend Horton Heat
Suicide Squeeze
TVT/WaxTrax Chris Connelly, Die Warzau, Ministry, Nine Inch Nails, Revolting Cocks, XTC, Sister Machine Gun