First, there are a couple of other muni golf courses in San Diego worth mentioning. Balboa Park Golf Course, located near downtown San Diego, has an 18-hole course and a nine-hole executive course, both of which recently received new greens and cart paths. The big course has great views of the city and Coronado. And scenic Mission Bay and Practice Center has a great 18-hole executive course designed by Ted Robinson. Located in the heart of the city, it’s the only golf course in San Diego with lights.
Closer to Torrey Pines on the north side there are several other great layouts open to the public. Maderas Golf Club, for example, has been voted San Diego's top golf course by the Zagat Guide for five consecutive years. Then there's the Tom Fazio-designed Grand Del Mar and Rancho Bernardo Inn, which has hosted numerous PGA and LPGA Tour events.
Of course if you visit the area, I highly recommend playing one or both courses at Torrey Pines, site of the memorable Tiger vs. Rocco duel at the 2008 U.S. Open. It's a bit pricey – non-residents can expect to pay three or four times as much as the locals – but it's worth it, considering the recent renovations by Rees Jones, the history, and the views from the bluffs above the coast.