LIRR Today featured an excellent article on the AVPS (Audio Visual Paging System) of the LIRR (those orange LED signs that give you the time your train will arrive). I found this part about how the MTA determines a train's time interesting (give or take 6 minutes):
The way the AVPS systems currently work goes something along these lines: the LIRR's TIMACS system (which stands for Train Information Management and Control System) times each and every train as it passes one of the LIRR's various interlockings. This system is built in as a layer of the signalling system and primarily works as an arm of the signalling system (there are other contingencies in place for trains that operate into dark territory, where there are no interlockings). At each and every timing point, the system notes the time and compares it to the time the train is scheduled to pass that interlocking. At that point, it can then determine, very accurately, how many minutes the train is late or early.
Read more if you are interesting in LIRR Countdown clocks as well as suggestions on how to improve them.