San Diego is a beautiful place.
A few things:
Cabrillo Marine Reserve is some of the most well preserved/protected tide pools in the country. Definitely a fun afternoon for someone who loves the ocean, but check the tide charts so you don't show up when it is inaccessible. It is the same thing as the monument Jake mentioned, I just know about the tidepools from working there for a while.
Stone Brewery is in Escondido, which is really close. I am not sure if you are into beer, but Stone is an awesome brewery and they do the whole tour thing, which is actually pretty fun.
Mission Bay is an awesome place to walk around and maybe grab dinner, or if you are a high roller, they have all sorts of dinner/harbor cruises so you can do both at once. San Diego Harbor is pretty cool too, as it is a military harbor. It is not often that you get the chance to see an aircraft carrier parked in the middle of a city. It really gives you a sense of scale as to just how freaking huge all the Navy vessels are.
I recommend skipping the trip to Tijuana. Too many severed heads in duffel bags these days...
