Here are some of my favorites in SD when I was there for grad school. I think of these places often now that I'm out east away from them. Just thought I'd share the info, enjoy them for me!
Adams Avenue Grill- great food, nice casual laid back kind of place where the locals eat. The menu changes weekly, but don't miss the waffle fries and the desserts.
El Zarape- with so many mexican options in SD, this small place has to be my favorite. All the basics, but you can get great tacos (including salmon and shrimp), and they have a nice burrito with chicken and mole sauce. What I wouldn't give for a carne asada taco right now...
Saffron- the freshest and one of the tastiest Thai places I've eaten at.
The Mission (both locations)- I could have brunch here everyday of the week and still not get tired of the place. Love their rosemary potatoes, chicken apple sausage, french toast, cinnamon buns, blackberry shakes...the list goes on and on!
The Brigantine- even though it's a local chain, they know how to do fish and seafood well.
Via Italia Trattoria- you can't tell by its location in a strip mall, but this italian place is absolutely authentic. The waiters are italian, the people at the other table are italian, this is the real deal. Love their pastas and pizzas.
DZ Akins- great deli and restaurant, especially for california.
Rubios- even though it's a chain, you can't beat their 99 cent fish taco promotion.
In N Out- another chain, but once you leave the west coast and no longer have access, you sure do miss the fantastic double doubles with grilled onions. Try 'em "monster style" too.
So that's my two cents. How's the new downtown stadium coming along?