The first graph presented is a take on E.J. Marey's graphical train schedule. You can do that with pretty much any agency that puts out a schedule (one of the D3.js examples uses the Caltrain info). A lot of agencies have standardized on Google's GTFS for this information.
The station entrance/exits can be harder to track unless you are required to tag off. In the Bay Area BART publishes this info, I think as an Excel file.
Realtime info varies wildly, but a number of agencies (including BART) have jumped on the GTFS Realtime bandwagon. Muni went with NextBus which used to have a publicly accessible API (and that use to "hide" very detailed info), but it looks like everyone's favorite conglomerate, Cubic, destroyed that when they acquired NextBus.
