I'm new to switching and know very little, but have been reading about it (scary). I have found several links that I have been saving, but have not really looked at any of them closely. Probably wouldn't know what I was looking at yet anyway? I will post a few for you to look at. Most of what I have been reading has been for HO and N scale, so some of these links are probably geared toward that instead of O scale.
Albion Software
CTI Electronics
DCC By Design - Not sure about this one?
Interchange Software
JMRI
NMRA Manufacturer's Software - Long list and not all switching related
ProTrak
Quaker Valley Railroad
RailOp
Signals By Spreadsheet
You know a lot more than I about all this. Some of these will probably not be what you are looking for, but hopefully you might find something, or maybe a lead to something else? Sorry if this turns out to be a wild goose chase.
Also another forum member posted a web based operation application that someone had made for them. They sent me a copy but there was a problem. They got the problem corrected but I have lost track of the poster and the thread. Maybe they will see this and reply. As I recall, some folks liked it. I am pretty sure it has been since the 1st of this year that this was posted.
I would be interested in following your findings if you find something good.
I have been reading a Model Railroader special edition or something about operations on model railroads and also 'Realistic Operation For Model Railroads' (or something like that) by John Armstrong (author is correct). I think some of the links came from these publications. I will look for the exact titles tomorrow and correct the post here.
Edit: You all probably already know of these, but actual titles were:
"How To Operate Your Model Railroad" Model Railroader Special Issue - Summer 2012
(Magazine like)
"Track Planning For Realistic Operation" by John Armstrong (Large size paperback book)