Enterprise Rent A Car, the largest rental car company in the country, has five locations in San Diego. Besides their office right outside the San Diego Airport, they also offer rental cars downtown, in Mission Valley, and in two locations in La Jolla.
There really isn't anything great about the staff or the cars at Enterprise, but they are still the only car rental business I go to. Enterprise is everywhere, there are always cars available, and it is very affordable. Whenever my car breaks down or I am on a business trip, I always rent from them.
I just moved to San Diego and had to transport a bunch of stuff from Northern California, but didn't want to have to rent a U Haul. I rented a mini van from Enterprise and it was such a convenient, fast, and cheap process. I think I saved around two hundred dollars not renting a U Haul.