Here is a list of links and resources which I find myself frequently drawing upon. Hopefully you will find it useful! Please feel free to suggest others in the comments below.
This page will be periodically updated.
Ward Maps, and their Massachusetts Transit Maps collection, (don’t miss their atlas collection, giving a block by block view of the city over the decades, such as the 1895 edition) and their sister site, Boston In Transit (don’t miss their track plan sets!)
Maps of the Boston Elevated Railway Company, archived at Wikimedia Commons
Public transport maps of Boston, archived at Wikimedia Commons
Amtrak Timetable Archive, 2008-present, maintained by Christopher Juckins
The Museum of [Amtrak] Railway Timetables, 1970-2016
Train timetables of the United States, archived at Wikimedia Commons — be sure to click through to the Boston & Maine, the New York, New Haven & Hartford, and the MBTA Commuter Rail sub-categories
Changes to Transit Service in the MBTA District 1964-2021, by Jonathan Belcher
Boston Street Railway Association
The Annual Reports of the Boston Transit Commission, 1895-1918, archived at Wikimedia Commons
Vanshnookenraggen’s MBTA Track Map
Vanshnookenraggen’s NYC Track Map
Vanshnookenraggen’s Chicago Track Map
Underground Station Diagrams — a colleague on ArchBoston has slowly been building diagrams of the underground layouts of various MBTA stations over the last several years
CartoMetro.com — highly detailed track maps of London, Paris, Toronto, Los Angeles, and dozens of other systems
Present-Day Data (Ridership and Performance), Studies, and Reference
MBTA Better Bus Profiles — in my (hot take) opinion, this is the most valuable collection of MBTA ridership data and analysis on the web, at least for non-professionals; it’s an extraordinary level of detail, balanced by easy-to-read analysis and summary
MBTA “Blue Book” Open Data Portal — get access to all the ridership data
The 2014 MBTA Blue Book — the last version of the “Blue Book” that was published in pdf form; if the Open Data Portal is a little daunting for you, this can be a suitable alternative in a pinch
Amtrak State Fact sheets, including ridership numbers per station
Christopher Juckins’ website, including regional Amtrak maps and the Amtrak Status Maps Archive Database, providing a wealth of data on Amtrak’s on-time performance
RIPTA Rider Survey Report — this is the only per-route ridership breakdown I’ve been able to find for RIPTA
NYCSubway.org — a treasure trove of photographs of transit systems around the world, as well as a long-running collection of NYC Subway track maps
Miles In Transit — lots of detailed detailed descriptions of many many bus routes and stations
The MBTA Vehicle Inventory Page
The 2018 South Coast Rail DSEIR
The Northeast Corridor Infrastructure Master Plan, including track diagrams for proposed expansions of the NEC
The Wayback Machine — can’t find an old schedule? Looking for an old map? Always check here!
Wikipedia’s List of colors by shade and List of tertiary- and quaternary-color terms — need to think of some colors beyond ROYGBIV (or ROYGBP) to name your transit lines? Look here for inspiration!