Surprised none of you have mentioned Open TTD
http://www.openttd.org/en/ which takes Transport Tycoon Deluxe and makes it even better in a lot of ways (incorporates a lot of the previous hacks and other stuff too that were for TTD).
You do need the original data files from TTD though to use OpenTTD
Locomotion was not very well received by the fan base mainly as it didn't improve much on TTD, and ignored all the fan made progress to it (including the most basic essential stuff such as presignaling and the like)
As for Railroads I am not aware of any major fan mods that fixed the issues. I don't think the devs fixed much (dig up the patch logs though). I never could get into that series myself