Neiman Marcus has a great selection, but the SA's upstairs seem to get a bonus for acting like asshats. I wish I didn't have to say this, but it's been true every visit. ( People who were in the Basenoter tour of shops back in April should remember the "Don't smell the fragrances!" guy, but there's always been one. ) The downstairs Men's section seems really nice, though.
Saks also has a good selection, and much, much nicer SA's.
Diptyque is really fun; I recommend it. I've always had a good experience there.
Barney's is perfumery paradise, and I can't recommend it enough.
Jacqueline perfumery is an interesting place and tends to have a lot of rare oldies.
Hermes & Chanel have boutiques nearby if your interest is piqued by the exclusives.
The best part about San Francisco is that all the stores are really close together, though some of them are kind of hidden away ( like Diptyque, down an alleyway ).
Have a great time!