I'll second the comment above that mentioned Old Town San Diego. Cafe Coyote is a good spot there for Mexican food but it's a really cool area to even just walk around.
Gaslamp quarter is also awesome for bars and restaurants. In Gaslamp, there's a seafood restaurant called Blue Point. Great food -- the Lobster Bisque especially.
Breakfast spot at gas lamp, Broken Yolk is fantastic.
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