Around town, there are a bunch of places to ride (some smallish)
-UCSD (there's a great eucalyptus grove that is perfect for cross
-Misc canyons around La Jolla/Clairemont (Rose Canyon, Tecolote, ...). Many of these are small, but can be combined with some road for a cool mixed ride.
-Balboa park near the velodrome and on over to hillcrest. There was a cross race here last fall.. most of it is great on a cross bike, though parts are a little on the rocky side.
A little ways out of town is the Big Laguna trail at mount laguna (about an hour east of SD). Beautiful ride, lot of fun.