As a native San Diegan I'll chime in.
I would avoid a day trip to Mexico, especially if you are taking two kids. TJ is a hole and wrought with drug cartel violence. Ensenada is about an hour drive south and I don't think that area is immune to the drug trafficking problems the border towns have. I would avoid Mexico all together. Completely unsafe and not a great place to go unless you really are in need of buying a blanket or a ceramic surfing monkey.
Long drive to SF but it looks like you have already crossed that off your list.
Cabrillo Point, Point Loma and Cornado Island are nice. A little touristy but what isn't. Old Town San Diego is cool if you are looking for historical San Diego type stuff to do. Gaslamp Quarter is great for numerous bars and restaurants and is right by Petco park if you want to drag the kids to see the Padres.
Beach is always a good choice but in March the water might be a bit cold.
More options here:
http://www.tailgatewiki.com/view.cfm/NFL%2...ocalAttractions
As a former Pacific Beach resident, the cold water is not that big of a deal in March, it's the hordes of very drunk Spring Breakers that should keep you away from the beach. If you still must go to the beach I'd advise going north of PB, maybe all the way up to Solano Beach (20-30 minutes north or so). PB, Mission Beach and Ocean Beach are almost unbearable in March although maybe this is just residual disgruntled resident feelings. Forget Mexico, it was a horrid place before the rise in violence
Balboa Park is a good day trip and if you can get away from the kids for a bit and play disc golf at all, Morley Field is the best course in Southern Cal.
Sea World, the Zoo, Legoland, Wild Animal Park have all been mentioned. They're touristy, expensive and probably crowded but will not fail to keep your kids in awe.
Haven't been down there since Petco was built but Gaslamp District is probably more of a date night without kids and there are some great restaurants.
I hear the Stu Seagal has his studios all decked out for tours so if you want to see Hollywood Lite you could tour his little dirty, corrupt stages or you could drive the 2 hours more or less to LA and go to Universal Studios or Warner Brothers.
I don't remember when the waves are good at Trestles, and if they're good it'll be crowded, but there is world class surfing there and it's less than an hour north. Also San Onofre campsite is just south of that if you want to camp on the bluff, or San Mateo is inland and a quick drive to the generally uncrowded beaches down there, as everyone's attention is on Trestles. If you go, careful of the nude beach which I think is Trail 5.
There's Old Town and Downtown, reachable by Trolley (which I would look into a lot for parking reasons).
Anyways, this was really just an exercise in what I miss from SD, though I certainly don't miss working at Stu Seagal (a savage thief and cutthroat turd).
Just remember, the further away from Mexico you stay, the better.