Also, wanted to add, depending on your length of stay, every Tuesday at Balboa park there are a group of museums that are free or almost free.
http://www.sandiego.gov/park-and-recreation/parks/balboa/free.shtml
If you're going in October, the zoo typically has kids enter for free all month, which is a good savings if you have kids.
I like going over to Coronado, paying to park at the Hotel del Coronado, and then you can go out to the beach and wander around the hotel grounds. They have a very good, but a bit spendy, snack bar out by the pool. And, an ice cream shoppe is there that's similar to Cold Stone.
There's a new Children's museum that I haven't been to yet. Once again, don't know if you have kids and what their ages are.
http://www.thinkplaycreate.org/ncm_visit.html
If you have older kids, no kids, or even younger boys, the Midway museum is great. There's a combo ticket for a harbor cruise and midway ticket and it's a pretty good all day price. Surprisingly for us, the cruise was very much enjoyed by all.
Here's a link for free in san diego...
http://gocalifornia.about.com/cs/sandiego/a/sdfree.htm
As for the Padres game, they have a program called "Park at the Park", where for $5, you get inside Padres park, but not seats in the stadium. They have picnic seating and you can watch the big jumbotron.
During the summer months they have a movies in the park program. Look in all different communities, as they have them all over. The one in our area is sponsored by the cable company.