People have already pointed out most of the highlights. Walker Bros., closely followed by the other Original pancake house locations, serves in my humble opinion the best breakfast in the world. The 49'er Flapjacks are phenomenal. They do other things well -- homemade corned beef hash, salami & eggs, bacon waffle etc. -- but it's madness to go there and skip the specialty pancakes.
Wishbone is also terrific. They do good Southern fare like cheese grits, but they also have more creative dishes like the salmon cakes. The buttery corn muffins with bits of cooked onion melting inside...heaven.