Courtesy the brilliant minds on the SVBC listserv and especially Margaret Okuzumi, ED of the Bay Rail Alliance and a very nice and friendly person:
Caltrain will tell you the bike rules, but those of us who use it every day will tell you how to do better than the rules and be a courteous bike commuter when using the train as part of your commute.
One thing we missed: don’t obstruct pedestrians getting on or off the train. Caltrain says pedestrians have the right to board and exit first. Try not to get in the way of a pedestrian or contact one with your bike — it could end in reprimand, anger, or injury. Sometimes simultaneous bike/ped boarding and deboarding is permitted by the conductors. If the stairs are divided unevenly, it’s bikes through the wide side unless you’re experienced and have a skinny bike, but if the wide side is on the south (pedestrian) side of the car, the pedestrians get to go first.