On the capitol corridors (unreserved trains making the 2 hour round trip between Oakland (or sometimes San Jose) and Sacramento, the seats are unreserved, and it doesn't seem to be a problem which train you ride.
I suppose if they were really full and there were no seats, then people would just sit in the aisles like they do on Deutsche Bahn's ICE trains--but I can't imagine they'd kick you off the train.
-Hayden