Great food in San Diego?
For Mex, I would do Hacienda de Vega in Escondido..Taco Shop..Las Quatro Milpas
Seafood...Fish Market Oyster Bar in Del Mar/Downtown SD..
Point Loma Seafoods.. local hangout but very popular with the tourists....love El Pescador for some of the best fish sandwiches in La Jolla.
Italian, love Baci's in Mission Bay area, expensive but delicious...some great restaurants in Little Italy but names are escaping me..
For seafood I recommend Blue Water on India St. Its not very touristy and they have really great fish sandwiches and fish tacos. Its a really casual spot, but the seafood is great.
For mexican, personally I recommend Jimmy Carter's Mexican Cafe. The food is pretty authentic, and it is really tasty. I usually get one of the specials, which normally consist of various mexican stews served with rice, beans and tortillas. This is also definately not a touristy place.
Based on my one experience at Jimmy Carter's (a couple days ago) on Washington St., I agree. Really tasty carne asada burrito. Everyone in my group ordered something different and everyone was happy (I've heard the one on 5th isn't as good). Super Cocina is also really good. South Beach in Ocean Beach has the best seafood tacos in town.
I haven't found a reliable Italian restaurant in San Diego yet, but I used to live in Italy so I'm probably a little more picky than most. I used to recommend Buon Appetito for decent Italian food, but a couple weeks ago I had a mediocre meal that broke some cardinal rules of Italian cooking (sauce-to-pasta ratio way too high, way too much meat IN the sauce, cheese that tasted like and had the texture of Kraft Parmesan, chicken on pasta).
I had some amazing seafood at Tapenade in La Jolla last week (Dungeness crab salad, Alaskan halibut in a basil emulsion), although I personally would avoid the lobster in Tahitian vanilla sauce. If you like sushi, Sushi Ota in Pacific Beach is the best in town, IMO.