Maybe I could throw in a good word for Caltrain - from San Francisco to San Jose (with a few trains to Gilroy). They're typically on time, although there are unfortunate delays to to "trespasser incidents". It's pretty clean, most passengers keep to themselves, and the employees are generally pleasant. They run 7 days a week, on holidays, and run a full schedule in both directions all day.
It has changed since they moved to a fare checking system. I think at this point most passengers use the interagency Clipper fare card, and fare checkers (who have a different job than the conductors) either ask to see paper tickets or use readers to check people's Clipper cards. I fondly remember when one would buy traditional punched tickets either at the stations with ticket offices or sometimes directly from the conductors. There were some stations that didn't have ticket offices and there wouldn't be a surcharge for buying on the train, or if it was a weekend or holiday where the ticket offices were closed. Then of course the tickets would be placed on clips near the seats in the traditional manner.
And I guess the kicker is that it's one of the last commuter train systems that allows riders to consume their own alcohol. The first time I'd ridden in a while was with my kid. And there were some groups that brought cases of craft beer to drink. Then when I asked a conductor about some of the stuff he witnessed, and he said some riders would bring bottles of liquor and they would be downing shots. I boarded once with a bottle of Corona (don't judge) and in my kid's stroller's cup holder. The conductor said "you're good with that, but you're supposed to fold the stroller before boarding."
