Ok read this thread a bit ago and was thinking on possible solutions.
First let me say I would only do this for an over veiw just to give every one an Idea how it looks and fits. For specific areas I would have seperate maps for detail.
The Idea is to give both a way to map and a way to give the gee-relation of living in a Cylinser.
First I used the obvious picture as a base for the designe elements
I then use paths and the path too selection to mark off my specific designe elements (three planes in perspective, with a central hub) I left the glass area blank or transparent.
After the general designe layer I chose one of the maping areas in this case the bottom plank. Selected the continuous region (in gimp use the magic wand) Make a new layer called bottom or somthing simular and fill with favorite grass collor.
Pertie much your going to have to work to get the perspective thing right
Each map section has its own serries of layers and it will allso have its own "flat" map. Bottom on bottom the upper right on the right side and the upper left on the left side leaving the top for the central hub and the deckplans if any.
After the initial picture mod you need to Scale the image the entire image gimp allows this under Image>scale Image; While doing this under the offsets keep clicking center this gets your original image in center giving spaces for margins.
After scaling created a new layer called bottommap then I went ahead and used the rectangular select tool to mark an area filled it with green
New layer filled with noise (gimp: Filters>render>Noise>solid Noise) play around with the settings and a judicious use of ctrl+z (undo) to get somthing you like. for the river make it its own layer with a pincile tool scratch out somthing you like then using the wand tool and having that layer selected copy it.
Create yet another layer paste the copied river rotate it so that it is vertical and use a perspective tool to aligne it with the perspective veiw thingy.
Map to your hearts content alternating between making the land forms on the flat then making a perspective version. For the other effects I would make layers under the map but over the back drop until you get somthing you like.
Maybe thinking about it from the inside would help... If you were a new arrival at the cylinder and had just downloaded a map of the facility into your Augmented Reality rig, what would it look like? It could be cut into rectangles, but rings in an exploding view are possible, Given the size of an O'Neil, the detail on the overview map only has to be enough to show major landmarks and topography...
Anyway, my two cents, I haven't tried one either. Yet.
In space...no one can hear you whine...
My Maps in All Their Glory