Southwest will offer you the most options into San Diego...74 flights a day. They are the primary carrier, as they are in many of the so cal cities. They don't fly into a lot of the major hubs however (Denver, OHare, Boston, Atlanta, DFW, Newark, JFK, LaGuardia, Washington Dulles) but will fly into cities nearby (Long Island Islip, Baltimore-Washington, Manchester NH, Providence, Dallas Love, Chicago Midway)
Delta has been cutting service to SAN as they closed their DFW hub. That being said, their fares are pretty competetive.
America West offers great deals into SAN.
British Airways has a nonstop 777 flight from London Heathrow for UK fans.
Air Canada also flies nonstop from Toronto.
Try all the travel sites, Orbitz, Priceline, Expedia...just remember that Southwest doesn't use any of those and you can only get their fare through their website.