I would bring back vegetables and fruit from the The Vegetable Shop farm stand (aka Chino's). Various notable chefs (e.g., Alice Waters, Wolfgang Puck) fly in their produce daily. They have fantastic strawberries, tomatoes, shell beans, herbs, greens, and more. (San Diegans love the corn, but I think Illinois has better corn at a better price.) If you like gawking at fancy estates, the drive out to Chino's takes you through the ritziest area in San Diego. Take the 5 to Via de la Valle. Go east a few miles, and turn right on Calzada del Bosque (just after you see The Vegetable Shop sign.) The stand will be about a half mile down on your right.
Mexican food in San Diego really isn't all that (especially compared to Chicago), but Super Cocina is very unique. The cooks' only experience is cooking for their families, so you get an interesting range of dishes. Two dishes from the steam table plus beans and rice will run you about $7. The neighborhood is a bit dicey (by San Diego standards), so most people go for lunch.
Super Cocina
3627 University Ave.
San Diego, CA 92104
(619) 584-6244
More on the tourist path is the Marine Room, mentioned above. They do a fantastic brunch. The cuisine is a little dated but nonetheless delicious, and the view is worth the trip in itself.
San Diego does sushi very well. If you like uni, make sure you have it while you're out here because much of the uni in the U.S. is caught in San Diego. Sushi Ota is a very popular option. You need a reservation, and try to sit at the sushi bar (preferably in front of Ota himself).
Sushi Ota
4529 Mission Bay Dr.
San Diego, CA 92109
(858) 270-5670
You also could try Sushi Dokoro Shirahama. The owner/sushi chef is pretty strict about his sushi, and no California rolls are allowed. The fish is incredibly fresh, though.
Sushi Dokoro Shirahama
4212 Convoy St.
San Diego, CA
(858) 650-3578
If you go to George's at the Cove in La Jolla (mentioned above), keep in mind that there are at least two restaurants in the complex: fine dining and the outdoor terrace. I've only eaten on the terrace, and that was some years ago. The food was nothing earth shattering, but the view is beautiful.
For local fish, I prefer El Pescador and Rimel's Rotisserie in La Jolla over Point Loma Seafoods. El Pescador is a tiny fish market that also makes some delicious fish sandwiches. Rimel's does various grilled items, including fish caught on their own boat. Others like Blue Water Seafood, but I've never been.
El Pescador
627 Pearl St
La Jolla, CA 92037
(858) 456-2526
Rimel's Rotisserie
1030 Torrey Pines Rd
La Jolla, CA 92037
(858) 454-6045
Blue Water Seafood
3667 India St
San Diego, CA
(619) 497-0914
For further recommendations trending towards the Asian and budget-friendly, check out
http://mmm-yoso.typepad.com. The restaurants on Kirk's "rotation" are quite reliable.