I can't recommend any hotels specifically in San Francisco (expect that to be expensive!), but if you're interested in staying further down the peninsula, I've stayed happily several times at Dinah's Garden Hotel, roughly on the Palo Alto / Mountain View border. They have some nice gardens, a coy pond, and some very good omelets for breakfast.

If you're heading up to the wine country, my wife and I randomly ended up staying at the Farmhouse Inn several years ago. The rooms are a bit over-the-top posh, and the restaurant is staggeringly good.