What are good locations for bird watching in the San Diego area?
The San Diego chapter of the Audubon Society has a handy web application here. There are also an events listing, field trips, info on the Christmas bird count, and more.
I would probably add the San Diego Botanical Garden in Encinitas (north of San Diego, near the coast). It's not a big birding location, but has a lot of different habitats.
Some of the best birding in the US can be found in the San Diego area and the County has a great, detailed resource for enthusiasts. To whet your appetite:
With most of California’s wetlands gone and developed, birding enthusiasts should know those wetlands remain here in the San Diego County region serve as the last refuge for many of the Western Flyway’s migrating birds on the way in or back from farther south.
That makes San Diego one of the premier destinations for birders from all over the world. As many as 480 bird species have been identified in San Diego County. In addition to this hot spot for birding, the Colorado River and the Salton Sea to the east also are prime bird-watching areas and within a day trip of San Diego.
Happy twitching in the paradise that is San Diego.
During my recent trip there I didn't get to try all that many locations but my favorite ones that i did visit were definitely Tijuana Estuary and Mission Beach. The highlight was perhaps a close encounter with a fishing Osprey right by the Tijuana Estuary visitor's center.
Taken from the Tijuana Estuary visitor's center:
The Tijuana Estuary visitor's center itself: