Pam-
My husband and I spent the the first couple nights of our honeymoon in SF. We had wanted to stay at the Phoenix--a hotel known for its rock 'n' roll guests. Unfortunately it was full so we stayed instead at the Laurel Inn. Both of these hotels can be found at <www.sftrips.com>
Someone made a comment about being Hotel Boheme in North Beach, which I think is a great hotel in a very fun location. The rooms are charming.
SF is so small that you could really walk anywhere. The Pacific Heights neighborhood (where we stayed) was a lot of fun as is North Beach. I would recommend finding descriptions of neighborhoods (in guidebooks) then picking one to suit your tastes.