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.
The also offer a free IndMan (Industry Manager) program that expands on the industries available in Waybills. It has data files compiled by the OpSIG. I've played with one file containing over 19,000 records. It comes with four files and I think there are over 40,000 industries in all. Many are newer, but you can filter by era. You can also enter your own... for instance, I could create interchange with a friend's railroad through this interface.
I have over 300 cars in the MiTrains database so far. I've played with Waybills. It is very flexible and I am please with the product.