This past weekend I purchased MiTrains & Waybills from Shenandoah Software.
MiTrains maintains a complete inventory of your locomotives and rolling stock. Tracks list price, actual cost, enhancements, condition (unbuilt kit, on layout, etc.), etc. Produces reports and prints your car cards.
Waybills is exactly that, it prints way bills. You enter your online industries and it supports color coding by switching area, which can aid the yardmaster in classifying work. For offline shippers, there is a sizeable database of real industries included. You can search these by car type, commodity, railroad, etc. You can then ship to or receive from these entities.