Mine are kept in a folder stored in a repurposed microwave cart/cabinet that forms part of my train layout. They are very accessible if needed.
I keep mine in a small two drawer filing cabinet.
Jeff
For any engine that is stored away, I keep the manuals in the original engine boxes, just as they came from the factory. As for the current "rotation" of engines that are out of their boxes and available for running on my small layout, I keep those manuals in a gallon-size zip-lock bag on a shelf under my control panel. In the event I have to reference something for a particular "in-service" locomotive, the manual is right there.
I think we all probably are pretty diligent about keeping the manuals in some format that protects them and makes them readily accessible.
With all due respect to one of my favorite brands of trains (MTH), perhaps MTH could solicit among us a list of units for which they do not have the manuals available and posted to their web site, and probably get copies of those from us to then update their site.
Just sayin.... Maybe another thread for me to start.
Have several 3 ring binders with dividers and plastic sleeves. Sorted by motive power (steam /diesel/electric), power, accessories, rolling stock, etc. Also maintain pdf files.