SD Native.
Either Alberto's or Sombrero's... Carne Asada Burrito. Thank me later.
Casa De Bandini in Old Town. Food is great and margarita's are huge.
Mount Soledad will provide you with an awesome 360 degree view. Grab some lunch, go up to the cross (if it's still there, I heard they might take it down) and enjoy a relaxing afternoon.
Kate O. Session's park in Pacific Beach. Another place to chill on the grass and enjoy.
Riding the old wooden coaster at Mission Beach is a kick in the pants.
Following the coast hwy up through LaJolla, Del Mar, Encinitas, is an awesome drive. You can start at south Mission Beach on Mission Blvd. and keep going till you have had your fill. Take the time to stop and take in the sights.
Walk the pier in Pacific Beach.
Coronado is nice. The trip over the bridge is always cool. Nice beach over there as well. You can head down the Silver Strand to Imperial Beach and hit the pier. If you don't want to do this whole deal, you can drive over the Coronado bridge and enjoy the view and whoop a u turn and go right back.
Walk the harbor down town by the Star Of India. The Midway tour is great as well.
Sunset Cliffs. Go there just before sundown and see how it got it's name.
If you like zoo's... The San Diego Zoo is awesome. Sea World is great too.
I'm sure I could go on for days on this one. If you choose any of the above you won't regret it. The Carne Asada Burrito is a must. Add some rolled tacos with guac. to that and enjoy!