Ive been to San Francisco more times than I can count, and this time we chose to stay at Annies Cottage and will definitely stay there again.
Essentially a basement flat in a quiet leafy street not far from Lombard st in the Russian Hill area, Annies is a quiet, restful and tranquil spot. Dont be put off by the corrodor through the apartment complex to Annies, as the front garden is beautiful as is the outlook from the rooms balcony.
There's some great dining nearby and transport is close so getting around is dead easy. When we stayed Annie was out of town and her house sitter who was really friendly took care of things, doing a great job.
My only (really minor) grizzle was the wifi, which struggled to deliver a robust connection, but I suspect that this is easily fixed and I would definitely stay again!
