Yes, sort of

I don't know if it directly answers your question but Google Maps view of the prototype AC&Y Brittain Yard was the starting point for designing my HO rendition of same. A track routing illustration was traced over the captured image to serve as a reference. Many modeling specific alterations were made to accommodate available space, model operations, available components, selective compression, etcetera but it all started with Google Map.

Nothing special, I suspect many modelers do the same.

Your overlay technique

isn't something I had even thought of. I will use it to take some of the best design elements to combine them together, perhaps into a hybrid of prototypical practices. However, my question is more toward using the non-operating features of abandoned routes or defunct structures by incorporating them into a layout. On one hand, that would go against the operating side of the hobby. But as a counter, it could add realism, especially for someone modeling current timelines.

time goes by

The Sudbury Division will be including disused and abandoned trackage.  There will be lots of clues of time going by on the layout.  We are in the process of building Wanapitei, which was a passenger station and siding in the steam era, but the station was torn down and the siding became disused as it was too short to meet diesel era freights.  We are modeling the siding, but it will serve no real function in operations; maybe we will park work equipment there sometimes.  There is also a spur just east of Wanaptei which served the Wanapitei Lumber Co., and this company was shut down by our era.  Our spur will head off into the bush with grass and trees growing between the rails.

Abandoned Trackage and Trestle Piers

I'm just getting started with the construction of my new layout.  One feature I plan to include is a short section of logging railroad trackage that has been abandoned.  The Spencer Lumber Company has procured trackage rights over a short portion of the nearly parallel Louisiana Central main in order to get across the Little River near the mill site.  Spencer ties into the LC main near the LC bridge, then exits the LC main back to their own ROW once on the other side of the river.

I plan to show enough traces of the abandoned trackage and the remnants of trestle piers across the river so the viewer can ascertain the former ROW.

-Jack

Planning from maps

I have used a wide variety of maps and on line mapping services to research my layout.  Since I am modeling 1900-1905, my railroad is the abandoned one. 

One caveat is just picking cool locations from a bunch of different railroads and areas will not necessarily make a good layout.  The context of a location is critical to a successful operation.  Putting in a really cool industry without the yard to support it might not be that fun to operate.  Including a nifty junction may be nice, but if you don't design the rest of the layout to support the traffic flows that the junction was designed to support, the junction won't be so nifty.  So try to identify how and why something is used.

Don't be afraid to flip or invert the track diagrams either, especially if you are freelancing.

I like to draw a schematic of the track plan that looks like you took the track plan and stretched it out so the main track is a straight line.  Then imagine that line is a string or a wet noodle and drape it around the footprint of the room or benchwork.  Don't be afraid to rotate or flip the benchwork in the room.  Sometimes the mirror image of a plan will work better.

It is often suggested that visually,

 it is very easy to model too much track in too little overall scenic space.  Unfortunately, abandoned track situations look like, and take up the same space as, working track.

So make sure you have room to do as much as you want of both.

I find it difficult to

I find it difficult to translate an Appalachian RR into a shelf/around the walls layout because the most prominent features, the mountains and buildings, take up so much space. 

Think vertically

I think it all depends on how you approach the situation.  If you think of a shelf layout as a layout on a shelf (logical, I know) then vertical scenery is hard to incorporate.  If, however, you get rid of the shelf and make the whole thing more vertical (except for the narrow ledge where the track goes) than you can get enough above and below track level to give the impression that the world goes up and down, instead of side to side.  I might even go as far as to ditch the idea of fascia entirely, letting the scenery apparently stop at the bottom edge.

Imagine a 12" wide scene, with track in the middle.  If the scene is flat, it's going to look like a prairie no matter what you have on the backdrop and fascia.  If, on the other hand, the entire scene were tilted to 45 degrees, with the track still level (obviously) in the center, now it looks like it's in the mountains somewhere.  Which mountains are defined by the choice of scenery.

Modeling "progress"

Since I model a regional that grew out of the Rock Island's ashes, modeling abandoned or out-of-service trackage is a big part of trying to capture the flavor of my prototype.  Here's Atlantic, Iowa's yard (model scene still under construction, with lots of static grass and a scratchbuilt depot (now the Atlantic Chamber of Commerce) still to come):

McClelland, IA and its abandoned elevator spur (Andy Brown photo):

Layout scene (again, still very much "in progress"):

Nice sky!

The grain elevator scene looks like there could be tornado weather on the way!

Sky

Thanks Rog.  It doesn't look imposing in person - at least no one has headed for shelter yet.  I was trying to go for the look of what I think is called an "updraft", but I'm no cloud expert.

Abandoned track

I plan to have at least one abandoned roadbed heading off the edge of the scene.  The turnout's been removed, but a short length of track for the spur is still there, overgrown, unconnected to anything.  That short piece of track will also be my programming track--hidden in plain sight.

I second the use of satellite images!

My small switching layout is based on a large industry in a small town (compressed to fit my space).  It's the Gerstenslager industry in Wooster,OH

Another place I've found interesting is the place I often go for work, the Freeport Center in Clearfield,UT (and other industries 10 miles north or south of that area). 

Copy and paste those into your address bar or search field and pan around but be careful...I have spent hours looking around Utah maps and come up with far too many ideas to complete in a lifetime. lol