We just spent a month in San Diego and I must report that we were somewhat disapointed by the food. Some of the fish places we sought out seemed to be living on their reputation and most places downtown (were we stayed) seemed over priced and some not especially good. The best meals we had, in my opinion were as follows:
The Prado (expensive, but we happened to catch a $20.06 for a 3 course meal special and it was really great).
The Fish Market (downtown) really fresh fish and not living on their reputation.
Kansas City BBQ (yes the "Top Gun" place) absolutaly no atmosphere and self admitted as "seedy" but great BBQ.
Jakes in Del Mar at their sunset specials at 4-6 with "Bistro Menu" at 1/2 price, but the sunset view is worth the money alone.
For Mexican food there are many, but I think our favorite was Los Pancho's (A chain I think).
San Tong Palace on Convoy St. for Chinise (we didn't get a chance to try some others in that area)
And the real suprise was Baja Rockin Lobster for the "Baja Bucket" (find a coupon and you get shrimp, "slipper" lobster tails, chicken and carne asada for two in a bucket with rice and beans plus a salad and salsa bar for less than $30 and it was pretty good to boot!)