Besides what has already been mentioned, I'd recommend these as well:
Rich G.'s Colton & Northern (Payware)
APH Lighting Enhancement Pack (Payware and I know I already mentioned it, but it's just that good)
Soo Line route (Freeware for the route, Donationware for the assets)
RW Tools (Donationware)
P&LE Route (Freeware)
And here's a few other sites I forgot to mention:
http://www.allaboardrails.com/ - Here's where you'll find all of Rich Garber's routes.
http://www.pikesproducts.com/14201.html - Free repaints for the Dash 9 and a payware pack that adds flashing ditch lights to them as well.
http://www.rstools.info/rw_tools.html - An absolute MUST HAVE, RW Tools is an awesome program that allows you to edit many different aspects of the game. A one time donation is all that is required.
http://www.sporbust.com/RS--Downloads.php - More free locomotive and rolling stock repaints.
http://alleghany.weebly.com/the-download.html - The home or Tori's WIP C&O Allegheny route.