In Regards to the SF Bay Area:
6th ave: Kind of a thrifty place. Great asian food nearby. I love Clemment Street. I recommend eating at King of Thai Noodle on the next block across the street.
Aqua Forest: Definitely go there but not on Tuesdays because they're closed on Tuesdays. Wed-Sun are the best days (IMO) GREAT seafood place up the street from it. Woodhouse Fish Co. What better way to complete looking at fish than eating some. I had an orgasmic crab melt though.
Aquarium Concepts: Gets better each time I've gone in, but I still think their Saltwater>Freshwater. Worth visiting.
Connies: It's on the way to Aquarium Concepts. Also steadily improving. Go browse the pond section in the back parking lot area. Best in the bay area.
Aqua Traders: Pretty sketchy. If there's one you could skip, you won't miss out on this place they're website is far more impressive. It's in a warehouse-type building, not much of a LFS feel.
Albany Aquarium: Very good store. The guy there, Evan, is the most personable LFS dude I've encountered. Pretty knowledgeable too. Livestock is expensive but looks very healthy (not that you'd be buying fish & shrimp on your honeymoon)
Aquatic Central: I've been in there about 3 or 4 times, hasn't impressed me yet. It's been quite a few months since I last walked in, but go in with low expectations. I just buy excel and that stuff.
Let us know how your experiences were. I've never been to the LFS in the south bay (Sunnyvale, Milpitas etc.)