San Gorgonio
As the tallest mountain in Southern CA, San Gorgonio is definitely a peak bagging must. There's a ton of fantastic single track, including some lesser known routes that can avoid the crowds.
San Jacinto
The second highest of the Big 3 peaks, San Jacinto has some of the best forest single track in SoCal. And there are several routes to the top other than C2C that still don't involve taking the tram.
Mt. Baldy
Easiest to get to of the Big 3, Mt. Baldy is a fun one. The front side can get extremely crowded, but still has some excellent single track. The backside though has one of my favorite trails in SoCal.
San Gabriels
Aside from Mt. Baldy, there are a lot of other great peaks in the San Gabriel range including Mount Baden-Powell, Iron Mountain, and Mt. Wilson.
Santa Anas
Not quite like the Big 3 mountains, but there's still some great trails closer to home in the Santa Ana mountain range.
Santa Monicas
The Santa Monica mountains are home to some of my favorite low mountain trails. They're no longer my daily stomping grounds for trail runs, but I still get back occasionally for some fun hikes.
San Diego
A little further South, there are some great low mountain trails in the San Diego area, including Cuyamaca Rancho and Palomar Mtn State Parks.