I love San Diego and usually take a trip there once a year. The Gaslamp is a great area for hitting up the bars and restaurants. It's by Petco Field (Home of the Padres) and the Convention Center. If you have a rental car,expect to pay a small fortune when parking it at your hotel or downtown. I usually stay in the La Jolla area or North County area.
What are your interests or hobbies? This would with making recommendations. I'd also check and see if there are any festivals going on.
Things I liked:
USS Midway is cool. I think it cost like $10 but worth it. If you don't want to go inside, you can take photos and walk around. They have various displays, sailor kissing statue, and various boats. We did a dinner cruise with Hornblower. They also do tours of the harbor.
Seaworld
Balboa Park
La Jolla Cove
Safari Land
Old Town San Diego
Olympic Training Center - It's located in Chula Vista, and not many people go to it, but I liked walking around it and seeing various athletes training.
Pacific Beach
I know people rave about In and Out Burger, but I recommend eating Mexican at various restaurants/taco stands. Try a California Burrito.