During the Year That Never Was, Martha Jones claimed to have gone to San Diego to collect one of the vials of liquid needed to arm the gun she was allegedly preparing to kill the Master with. (TV: Last of the Time Lords)
San Diego was one of the cities suggested by Diana Goddard to leave Henry van Statten after she ordered for him to be taken away, his memory wiped, and dumped "someplace beginning with S." (TV: Dalek)
Beginning in 1970 and continuing into the 21st century, the city hosted the popular San Diego Comic-Con each summer. Over the years, several incarnations of the Doctor and a number of companions have attended the event, occasionally thwarting evildoers in the process (COMIC: Convention Special, Selfie).
Though it's possible that a real world location doesn't exist in the same geographic space in the Doctor Who universe, such cases are few and far between. Thus, the map at right is probably a good indicator of the DWU location of San Diego.