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Starbucks at Laurel Height is open 24hr (California and Laurel St, http://www.yelp.com/biz/starbucks-san-francisco-132).

It is hard to find seats before midnight, as it is full of students, but it is as nice as a starbucks get.

Since it is so popular, starbucks tried to open another 24hr location close by, but there was a lot of opposition from local coffee places, so they didn't get a permit.

http://www.quora.com/What-coffee-houses-in-SF-are-open-after...

http://www.quora.com/What-are-good-public-places-to-laptop+w...

The Summit opens till midnight on most nights, which is still not as late as I'd like. It's really surprising, to me anyways, that this town really doesn't have a late-night culture.

Starbucks in San Bruno is 24 hours and has free wifi. Only drawback is it's really hard to find a seat in the evening as there's a bunch of students studying.