Smart Waypoints is a mod that enables waypoints with special names to control trains that go by, skipping around their schedule.
This mod does not add any new items or technologies to the game, its functionality is available from the first train stop you build.
Note that this mod was written in an afternoon, and due to limitations within the game, is a little odd to use. It's intended mostly as a proof of concept, but if you get some use out of it, that's great. Honestly, it took me almost as long to write the readme. :)
How To Use
Give a train stop a name like /ACTION/SCRIPT
, and then add it to a train's schedule. For more, go look at the Readme on the GitHub page. Seriously, this mod is a little complicated.
Discuss at the forum thread, or download the example map there to see the mod in action!