Hmm...sounds like I definitely need to get myself to the next SFBAAPS meeting. Was talking to another fellow forum poster this last weekend and he was talking about it also.
Aquarium Concepts is definitely a reefers' bread and butter. The selection of plant really isn't the best, but they price some of them for extremely cheap every once in awhile. The owner there, Ken is a pretty nice guy, and is willing to order for you if there's something that you're looking for (where I got my Synodontis petricolas from).
Atlantis Aquarium in Fremont is really only good for the saltwater stuff, and that's limited also. The owner there, Brian, is a pretty cool guy overall, but he's not in the shop all the time and has a limited amount of time when he is in there. The best thing about the place however are the fish in the display tank. Those tigerfish are just awesome...
If you're interested in saltwater however, there's not really a better place in the area than Tropical Paradise in San Leandro. Great selection, but all salt. This is where you wanna go if you're interested in the more hard to find corals (frags galore, clams, and just about anything that you can think of).