This one is my favorite -- this is where I bought the fancy shmancy stuff I sent my niece when she was a baby http://www.mudpie-sf.com/
But I would say that in general you'll find lots of great baby stuff (fairly expensive, though) if you wander around Union Street (not Union Square) or Hayes Valley.
I pass a couple of maternity shops on my way to work but I have to admit that I don't focus on them closely LOL