I mostly go to the nearby petco but I'm guessing thats not what you had in mind. I've been to so few LFS around here that I can give you the run down on each one. I buy most of my stuff, including fish, from online sources.
Nature Aquarium, Santa Monica ave., Santa Monica
Run by a Japanese immigrant, he totally goes for the ADA style. Has the best collection of freshwater fish and plants I've seen around here. Lots of the fish are unusual, don't remember any rare plants.
Allan's Tropical Fish in Venice
Good prices are the main attraction, lots of choices for food and equipment. The freshwater fish collection isn't that great and is very variable. Sometimes they will have something unusual but not regularly.
Medusa LA, pico blvd, West LA.
Mostly saltwater and herps, biggest collection of coral I've ever seen in a store. Small freshwater section in back, a couple unusual fish, not much. But the owner really knows his stuff. I treat this place as a small, free museum. : )
Aquarium and Pet Center, Wilshire blvd, Santa Monica
A lot of high end saltwater fish, some fresh but not a lot. Might have some unusual freshwater fish because they tilt to the high end, but I don't go there a lot.