Been thinking about moving there for some time now. Not into mobile apps or social networking sites, just a very strong backend developer (search engines, machine learning, etc...)
San Diego is home to a number of big name tech companies such as Qualcomm, Intuit, and Teradata. There are also a lot of defense and biomedical companies as well.
I'm not too familiar with the startup scene, but there definitely is one. I've seen some familiar names at many of the events (like Flud) and people routinely try to hold hackathons and other competitions like Startup Weekend.
One of the biggest differences I noticed was how fast and often people in the Bay Area switched jobs. I knew one person who left after a year at this company, and the makeup of my whole team actually has changed significantly over the past year. This probably has to due with how many tech companies and startups there are in the Valley, but in San Diego you'll find most people will stay with a job for a number of years before even considering about moving.
Haven't looked at many companies, buti like what Opera is doing.