They're three I usually go to. My local one, Comics Conspiracy, is the smallest of the three, but is wall-to-wall-to-ceiling comics. They have nearly everything, and if they don't, it takes about a week to get. You get an automatic 10% discount, plus another 5% if you're military. Bags and Boards are free with purchase.

My home away from home is A-1 Comics in Sacramento. Same variety as Comics Conspiracy, yet maybe more indy stuff. No automatic 10%, but I still get the 10% military. Bags and Boards are a nickel a piece. TPBs are 10-20% off all the time.

The one I occassionally go to is Comic City, down in San Diego. Medium-Sized store with same variety, and a big, big back issue storage. Signing up for pull boxes is free and you get 10% off, and a 15% military discount. Bags and Boards are a dime each, though. You might see some local talent in there, mostly Wildstorm staff; that's how I met Jim Lee when I was 12.