The Beach: this may seem obvious. Well, it is I guess. You can go to the beach and have a great time without spending anything. We spent most of our beach time at La Jolla Shores and loved it. We did venture to other beaches and I have to say, they were all good. I guess it depends on what you want to do but I love that La Jolla Shores has a playground and a grassy area so you can set up a tent or shade umbrella. It does fill up quickly on the weekend, so get there early. Parking can be tough.
Balboa Park: What a park! It is seriously the largest park I've ever been to. It has museums, gardens, performances, a beautiful carousel, a miniature railroad, hiking trails, oh and the zoo. The first Tuesday of every month the museums are free, so you may want to plan your vacation accordingly. You could spend all your non-beach time here and have a wonderful vacation.
Other places you may want to check out would be SeaWorld and LegoLand. I did go to SeaWorld and it was fun. I'm sure it would have been better with kids. I didn't go to LegoLand but I can't imagine a kid not having fun there.