Personal opinion, best burger in San Diego is at Rocky's on Ingraham street.
Western Steak Burger on University Ave is pretty darn good too but points off for not having beer and being cash only.
Went here a few weeks ago by accident and it was great. Good food, good service, not too expensive, live music and that day the $5 crab cakes on the happy hour menu were as good as any I have ever had. South Park Bar and Grill San Diego Live Blues and Jazz Club
Best burrito in town: surfin california at Lucha Libre off the 5 and washington.
Breakfast - try out Hash House a Go Go, the Tractor Room (pretty much same menu, same owner), or the Broken Yolk in PB or downtown and bring your appetite, huge portions at all of them.
Agreed - any ghetto looking taco shop will be better than ANYTHING you find out-of-state. I can't for the life of me understand why good Carne Asada Burritos don't exist on every street corner in the world.
There's a AWESOME seafood place ($$$) called Truluck's in La Jolla.
Wife and I went to Fat Tony's off Clairemont Blvd and it was delicious. Ballast Point beer, pizza, wings, garlic bread... They dropped a Groupon today too. $10 for $25. Go get some.