Off the dome:
Red Hot Chili Peppers w/The Mars Volta (Oakland Coliseum)
The Beastie Boys w/Talib Kweli (Bill Graham Civic Center, SF)
Z-Trip w/Black Sheep & Goldenchyld (The Grand, SF)
Mos Def w/Blackalicious (Berkeley Community Theater)
Kraftwerk (2004 @ The Warfield in SF)
Rock the Bells 2006 (Wu-Tang, De La Soul, Zion I, Redman, etc.) (Shoreline Ampitheater, Concord CA)
Del w/A-Plus, Mike Relm, Psalm One (The Catalyst, Santa Cruz)
Dan the Automator w/A.G., Casual, Chali 2NA, and Common Market (The Catalyst, Santa Cruz)
The Offspring w/Cypress Hill & MxPx (The Warfield, SF)
Guitar Center Spinoff / Stones Throw 10 year anniversary party (Great American Music Hall, SF)
Massive Attack w/DJ Shadow (The Greek Theater, Berkeley)
A TON of Jazz shows including Branford Marsialis, McCoy Tyner, Joe Henderson, Bill Frisell, Paul Motion, etc.
And a lot of shows I wish I could have gone to but they were 21+.
I'm jealous you got to see Rage Against the Machine before they broke up.