Responding to myself ... ummm ...

Here are the spots I know of (currently operating lines) where RR crosses or operates in the San Andreas Fault:

- UP at Chittenden/Logan
- Metrolink near Palmdale
- UP and BNSF in Cajon Pass
- UP Indio to Yuma (the "fault" is a system of breaks throughout the Salton Trough in that area, so it's hard to say exactly where the actual San Andreas is crossed; the RR operates within the fault zone as much as crosses it)

Are there others?

I don't count the Hollister Branch as crossing the San Andreas. Hayward/Calaveras, yes, but the "official" S.A. is away from Hollister proper in the hills to the southwest.

If you want to throw in expired lines, you could probably add a few more, e.g. NPC/SP from Los Gatos to Santa Cruz, arguably NPC from Olema to Pt. Reyes Station, Hollister Branch in its original incarnation (to Tres Pinos). Lumber lines on the N. Coast, like were there rails in the Gualala area?