One of my favorite bookstore / cafe combinations in the whole world is Books Inc. I used to come here back when I only visited the Bay Area; I'd drive down from wherever I was staying, hang out next door for an hour in the fantastic used bookstore Bookbuyers, then wander over to inspect the new offerings at Books Inc before finishing off in the cafe upstairs.
It didn't just have good, sweet, frozen coffee-flavored beverages, it had a great upper seating area which was conducive to kicking back and working on a problem. I've written a lot of words and drawn a lot of drawings in this cafe.
There's also an art gallery lining these walls, which my wife has shown in a few times. It really makes this a fun, exciting place to hang out and eat, drink, read, and write.
But as always, the ultimate test of a coffeehouse is the ample selection of power strips in which you can plug your laptops ... wait, what? Seriously, the ultimate test of a coffeehouse is the coffee ... and I think Caffe Romanza passes with flying colors:
Did I mention the Mocha Frappe? Get yourself here.