Big Bear
Big Bear has a little too much city to make it feel like remote mountain trail, but the lake scenery is definitely nice, and there are some great stretches of PCT in the area.
Mt. Baldy
The closest, legit SoCal mountain is a great spot for trail running. There's the peak at 10,000' as well as plenty of surrounding lower peaks. But the best options are the lesser known trails that avoid the crowds!
Mt. Wilson
Mt. Wilson is the San Gabriel version of Santiago. Roughly the same altitude and terrain, but generally better singletrack. Also typically more crowds. But as always, there are the less used hidden gem trails.
San Gabriels
There are plenty of other great areas in the San Gabriel mountain range, from Crystal Lake and Iron Mountain in the South all the way to Tujunga Canyon at the Northern end of the range.
San Gorgonio
The highest SoCal peak at 11,500' has plenty of single track and is the place to go for alitude training. I have done more hiking and snow trekking in the area though, so there is stilll plenty of trail running left to do.
San Jacinto
The second highest of the SoCal Big Three at 10,800' has several great routes to the top. Some of the best are better suited for hikes, but there is still plenty of great trail running to be had.
Santiago
Santiago Peak in the Santa Ana mountains is a go-to spot for some low altitude mountain running. 17 miles and 4,700' of gain always makes for a great training run.