I can do some more research, but things are a little lean for free camping in the area, depending on the season and distance from the city. Anza Borrego Desert State Park and the nearby BLM land are excellent and free, but too hot most days come late spring to early fall. There is precious little dispersed camping in the mountains - there are a few areas near Mount Laguna, but you'll need an Adventure Pass as these are in Cleveland National Forest land.
If you're just looking for a place to stay a night while passing through, I know at least two of the local Indian Casinos allows overnight camping in their parking lots (much like the Wal Marts, etc.)
For cheap but not free, then the State Park campgrounds are a good bet, though hit-and-miss for availability. During summer, the beach campgrounds will be filled to capacity on weekends, and nearly full mid-week, but you can typically find a spot mid-week during the shoulder seasons. The mountains have several good campgrounds that are good spring to fall, and you can generally find a spot except on holiday weekends.
North of San Diego in the San Bernardino National Forest, there is a whole network of free "Yellow Post" camps that are totally primitive, but beautiful. Not recommended during winter (many roads closed to prevent damage while wet/snowy), but otherwise good. I'll point you to an excellent collection of those.
Let me know how long you expect to be in the area (and what season), and I'll try to get a list of recommendations together for you.