Damn, really? I've been craving a good bagel shop since I moved out here.
There's "The Bagel Bakery" up in SOMA that has almost decent bagels. But its way too out of the way to get a few bagels for the weekend.
1. For me, this was Nervous Dog Coffee down in Bernal Heights (30th-ish and Mission). Take a look on yelp for cafe's. Ignore the ratings, since they'll be based on the coffee they serve, not bagels.