My pick for Mexican is Mama Testa's Taqueria in Hillcrest. Most Mexican places in San Diego (at least in downtown and north) serve your basic, boring Mexican-American fare, but Mama Testa's focuses on regional versions of tacos. The tacos come in a number of forms - soft, fried, steamed, and stewed. All are delicious - you really can't go wrong.
Mama Testa Taqueria
1417 A University Ave.
San Diego, CA 92103
(619)298-8226
Perhaps unsurprisingly, there are a good number of restaurants in San Diego where you can get very healthy food. (Before I moved here, I wasn't one for going out for healthy food, but when in California . . . ) One of my favorites is Rimel's Rotisserie in La Jolla. They often run specials on local fish. I like to get the rotisserie chicken with sides of jasmine rice, black beans, and green chili garlic sauce. It all sounds simple, but the chicken is juicy with delicious, crisp skin, and the beans have a nice (chipotle?) flavor. It's also a relative bargain for La Jolla - the chicken combo plates are under $10. Another inexpensive option for La Jolla is El Pescador, which is a combination fish market and cafe. The grilled fish sandwiches are especially good.
Rimel's Rotisserie
1030 Torrey Pines Road, Suite E
La Jolla, CA 92037
(858) 454-6045
El Pescador Fish Market
627 Pearl St
La Jolla, CA 92037
(858) 456-2526
San Diego does great breakfasts. There is a "chain" of restaurants called The Mission that describes its cuisine as Chino-Latino. The Chino part of that equation comes out more at dinner time. For breakfast, the cuisine is heavily Mexican with some American fare thrown in. I like the platas tortillas - scrambled eggs with black beans, scallions, sour cream, salsa, and fresh tortillas. I typically go to the Mission Coffee Cup in La Jolla. If you want an extremely fancy brunch with an incredible view, try the Marine Room, also in La Jolla.
Mission Coffee Cup Cafe
1109 Wall St
La Jolla, CA 92037
(858) 454-2819
The Marine Room
2000 Spindrift Dr
La Jolla, CA 92037
(858) 459-7222
You didn't mention Japanese or sushi as cuisines of interest, but I have to note that San Diego has some pretty good sushi. The uni is especially good - much of the uni served throughout the U.S. is caught in San Diego. My current sushi bar of choice is attached to a Korean restaurant called Buga. (If you like Korean barbecue, Buga does a good job of that too.) The fish is as fresh as any other place in town (we especially love the hamachi. My husband eats a lot of sushi, but we typically are able to get out of there for $60 pre-tip, even when we order uni, giant clam, or other more expensive items.
Buga
5580 Clairemont Mesa Blvd
San Diego, CA 92117
(858) 560-1010
An excellent resource for San Diego dining is the mmm-yoso blog. Kirk has great taste.
http://mmm-yoso.typepad.com
You have to go to at least one beach while you are in San Diego. A really beautiful one is Torrey Pines State Beach, which is between Del Mar and La Jolla on Torrey Pines Road. Another popular beach is La Jolla Shores, which is in, you guessed it, La Jolla off of La Jolla Shores Drive. Coronado Beach is also popular and is on Coronado Island. It is a bit closer to where you will be staying than La Jolla, though.