When this thread started, I wasn't sure how far underground we were digging. Looks to me like it's not very far, as most of the bands named here had (or still have) what I would consider successful music careers. With that, here's a few bands I like(d) a lot from a similar, just barely underground level:

Mudhoney (the original and best grunge band, IMO), Superchunk, Built to Spill, Son Volt, Wilco, Rocket From the Crypt, Fugazi....

Can you tell I went to college in the '90s?

Anyone who needs their faith restored in modern rock needs to check out Wilco. Just do it. Every member of that band is as good at what he does as anyone. Nels Cline (lead guitar) and Glenn Kotche (drums) are ridiculously good and have unique styles. They've been at it for almost 30 years, and I've yet to tire of their music. Really, really good live shows. Hardly underground, but not a household name either (though I don't know why not).