Find any theater that that has THX certification.
Here in the Bay Area, I know of Century 20 Great Mall (Milpitas, CA) and Century 25 Union Landing (Union City, CA) that have every screen with full THX sound system certification.
I believe a couple of theaters in San Francisco have THX certification (AMC Kabuki 8 has a couple screens that have this certification and the Coronet definitely has it, too). I'm not sure if any of the screens at the Sony Metreon are THX certified, though.
I love the two Century Theater complexes mentioned above because they have excellent picture quality, great sound quality and stadium-style seating with great sightlines.
Metreon's larger auditoriums are excellent in terms of sound quality. I believe all auditoriums are THX certified. Brenden in Vacaville is a good suburban theater- all THX certified, only about 4 years old, with stadium seating and 16 screens. The prints do get scratched after a gazillion showings a day, Jesse!
The Coronet has a big screen, but I find the sound to be a little thin (because the auditorium is really big- 1000+ seats I'm sure) I'm also pretty sure it's -not- THX certified.
AMC 1000 Van Ness is so so...I think 3 or 4 auditoriums are THX certified...sound was very thin compared to Metreon when I saw Ep.2 a few months ago in both places.
The Century Theaters mentioned above sound good, never been there myself though...
If you can get into the screening room at Skywalker Sound, that's probably the best theater in the Bay Area...with the Pixar Theater in a close second in Emeryville. (my co-worker is watching TTT at Pixar tonight!)
I'm sure I'll think of more...(I've only been here for 4 years, if you'd asked about NYC, I'd give you a list a mile long!)
-Dennis
AMC Mercado is awesome on their 2 biggest screens. I assume Century at Great Mall is Awesome as its brand new and THX certified. I'm going to see the Two towers there since Century will accept the movie cash. I'l probably see it again at Mercado to see how it compared. I saw FOTR at Mercado and it was unbelievable. Most of the other theaters in SJ are pieces of crap that are at least 20 years old. I haven't been to any others in SF or around the area. Usually if the theater is new it will be good.
I suggest the Century 21 and Century 22 theatres in San Jose. They use the big Altec A-4 speakers but fully updated with the latest drivers and Bi-Amplified as well. I find these to be the best sounding theatres in all of bay area.
If you ever venture north of San Francisco there is a theatre called "The Cinema" in Corte Medara which is also nice sounding.