I love Crush Comics & Cards, particularly for its back issue collection. Most of the back issues are $.50 to $1.00 with more current issues and Silver and Bronze age stuff being higher, but VERY reasonably priced. What seperates these $.50 and $1.00 bins from other stores is that it's organized by Publisher, title and in sequential order. I go there with my list of things I need and have completed runs and filled in gaps. It's a great store.
I go to several comic book stores, but Comic Ink in Dublin gets the bulk of my business, including the coveted weekly new comic book buys. Why? The owner Lennie. The man really cares about his customers, providing fantastic sales and inviting people to comic convetions. He takes time to get to know you. He's knowledgeable and passionate about the things he sells and, if he doesn't have it in stock, will order it for you. It's a place where you feel at home. Aside from that, he's got a fantastic selection of back issues and action figures which ain't a bad thing for a comic book store. When in Dublin, CA, definitely check out Comic Ink.