UC Cyclery is good, very helpful when you're searching for parts; I can't speak about the service department, but everytime I'm there, the group is busy.

For the past six months I've been visiting Mission Hills Bikes, on Washington St (only 15 - 20 mins from UCSD). The mechanics are VERY knowledgeable, super helpful, and are friendly. The service prices are very reasonable, as I've had three recent service requests and each one was priced well-below what other shops quoted me. I won't go anywhere else.