Cafe Wannabee, at the corner of NE 52nd Ave and Brooklyn Ave NE, is already one of the best coffeehouses in the U-District. The drinks are cheap and tasty (a 16 oz mocha will run you $2.50), and they also offer pastries, sandwiches, and cookies. For the computer-toting individual, they offer free wi-fi.
However, the best thing about Wannabee is the atmosphere. The baristas and Wally, the proprietor, are friendly. The cafe's tables, custom designed by Wally, have different interactive or creative features. One table has a flat-bottomed bowl set into it, containing a large amount of tiny brass pieces. You can build neat little sculptures in there while you sip your coffee or hot chocolate or eat a pastry.
Wannabee has several bookshelves crammed with an amazing assortment of used books. You can buy these books, and from my brief perusal of the prices, I found them to be quite reasonable, even on the cheap side.
I very much recommend Wannabee if you're looking to enjoy a comfortable and friendly cafe atmosphere.