Bay Area rail operations on the Capitol Corridor are normal. As for the rest of California...
Train 6(9) derailed on Donner Pass causing the train to be stuck in the snow all night. The train was able to move again eventually after a crew could get there through the snow. The train cut it's trip to Chicago (CHI) short and returned and terminated at Sacramento (SAC). Service on the California Zephyr has now resumed with 6(10) departing it's orgin of Emeryville (EMY) 7 hours, 31 minutes late. The train is currently in Salt Lake City (SLC), 16 hours, 43 minutes behind schedule. Trains appear to be losing 4 hours crossing the Sierras. Train 5(9) is expected to be in tonight around 10:16pm, around 5 hours behind schedule, however I expect an arrival around midnight-1am.
In Southern California a large sinkhold near Gaviota and multiple rock slides near Santa Barbara have caused all Pacific Surfliner service north of Los Angeles (LAX) to be cancelled. In addition all Coast Starlight service is operating out of San Luis Obispo (SLO) with bus service between SLO and LAX, however due to highway 101 washouts no bus service is provided to Simi Valley, Oxnard, or Santa Barbara. Train 14(11) out of SLO should arrive in the Bay Area on time. UP is working to fix the damage.
The storms have taken their toll on Amtrak services throughout California. The Bay Area has been spared, however now that I think about it, during the first wave of storms around New Year's power was knocked out to the signals between San Jose (SJC) and Oakland (OKJ) and the yard (just north of OKJ adjacent to West Oakland BART station). UP had flag men in place all along the line, however Coast Starlight and Capitol Corridor trains faced significant delays between EMY and SJC.