I stumbled upon this site a couple of days ago and thought Id add my 2 cents about the chow of my hometown, San Diego.
San Diegos signature food (by way of San Felipe, Mexico) is the fish taco. They can be found everywhere, but eat them at Rubios, a fast food chain that got its start here. Rubios has an extensive Mexican menu most of it good try the chicken quesadilla.
In the Mexican takeout category, Robertos and its cousin chain Albertos also serve good chow. The carne asada burrito at 2:00 a.m. is especially good. The Robertos on Carmel Valley Rd. in the Del Mar area is great because it has picnic tables with a view. Note: the success of the aforementioned chains has led to the fact that almost every small Mexican take out restaurant has the suffix berto in its name. For example: Alibertos, Humbertos etc. etc. Some of these are good others not so good.
For standard sit down Mexican food, I agree that the Old Town Mexican Café in Old Town is excellent. Order the carnitas and get there early in tourist season.
As for burgers, the In and Out chain serves great ones. Fresh ingredients, great fries, great shakes. And, if you are in need of souvenirs buy some of their t-shirts, the shirt of choice of the surfer crowd at least the post 30 er 40 year old ones I hang with.
Ocean Beach which hasnt changed much since the late 60s is home to one of my favorite hamburger joint, HoDads. Great burgers, fries, and shakes with an atmosphere similar to the beach joints of my youth.
For walk up sea food try Point Loma Sea Food on Emerson St.. Have a crab cake sandwich and enjoy the view of the bay.
As for a pizza try, Bronxs Pizza on Washington St. Excellent New York style pizza.
Well, Ive blabbered enough. Ill share some of my favorite sit-downs later.