My top 5:
Tom Petty at the Fillmore in SF in 1997. So good, such a great venue.
MXPX in the basement of some bar in Tucson in 1998. Growing up in Tucson, I'd never seen a basement in any establishment. Throw in a bunch of punk kids running around in a pit, in the basement, in the middle of summer. Dumb idea. Lead singer ended up blacking out in the middle of a song b/c it was so hot in there.
Pearl Jam in the Veterans Coliseum in Phx. around 1998. First time I saw them, and they were amazing.
Jimmy Eat World at the Rialto in Tucson in 2002. Probably my favorite band, at my favorite old school theater-style venue, in my hometown.
Rage Against the Machine at Glen Helen Amphitheater in San Bernadino. Greatest/scariest show I've ever seen. It started with the fact that it was a rap festival that usually had 5000 people, but then Rage decided to play and it got moved to a 65,000 capacity outdoor venue. You had a majority of people who wanted to see Rage, but they had to sit through 8 hours of rap (not really the same fanbase). You also had 65K people all with general admission, but the lower bowl of the amphitheater had 10,000 seats and no system devised as to who or how many people got those seats, which led to security/fan issues. And it was hot as crap out. Needless to say, when Rage came on, there were bonfires everywhere on the lawn, helicopters flying over head flashing their lights, and then Rage coming out and just making the place explode. Amazing.