El Cerrito, CA
There's something rather satisfying about supporting independent bookstores, especially when they're located directly across the street from a giant corporation vying to outsell them. Pegasus is smart and clean, friendly atmosphere with a huge selection of alternative magazines, used books, and even a bit of music.
Arinell's pizza comes more highly recommended by my friends than I (I'm a zachary's girl myself) but if you're on the run, its cheep and pretty good. Miles better than the chains.
One of the first things I do every time I come home to Berkeley is hit the cheese board. Their pizza is one of the things I miss most about the bay. . . cheap, gormet, and an excellent business to support, (one of the first collectives in Berkeley, and a shining example at that) the cheese board is universally highly recommended.