It's nice to see a few of you mention Toad. The lighter side of alternative but well-written, poetic, angst w/ edgy guitar. And the GBs influence over airwaves and colleges is worth noting.
What about NIN or the Verve (are they 90s?) Or Whiskeytown. (not enough albums?) Lemonheads or James.
I like Midnight Oil too, but not sure if they would make the best?
I agree Smashing Pumpkins, PJ are clearly missing. And, interesting point about alternative becoming mainstream. Although I'm not a die-hard fan, Counting Crows, Live, Goo Goo Dolls, Green Day, Better Than Ezra, U2, and Brian Setzer, etc. were dominating the charts. This list is more "indie" vice charts so I'm probably getting off track.
I agree with most, but also wondered about Tom Waits in first. That's a bit of writer's brown-nosing if you ask me.