I have a binder where I keep all my engine and accessory manuals. These are handy when changing bulbs, lubrication points on engines, etc.
I also have a few binders for my layout design. One binder specifically for my signal system (I have about 57 signal lights on the layout, utilising over 80 circuit boards and a few thousand feet of phone cable). Another binder is for my layout design, where I have kept my original design sketches.
I am currently creating a design record in an XLS file, where I have my naming standards, wire standards, terminal block design, etc. The xls file contains the terminal block backing paper design (this creates a colour coded sheet with wire names that goes behind the terminal block and shows you where each wire goes. You match the terminal block backer name with the wire label name. Very handy when a wire or 2 comes loose)
I colour the paper backing label with the wire colour, making it easier to wire and understand where things go, without always needing to read the wire label. I use telephone cable (Red, Yellow, Green, Black) for my low voltage connections, so the label colour method helps a lot.
I am creating a single XLS file, with all my design notes and wiring methods, naming standards, design ideas, any wiring modifications I make to an accessory, how I use the various transformers, anything that will help someone understand my layout. This puts everything in one place. I have numerous tabs in the xls file for different things. This has been quite helpful for reminding me what I did a number of years ago. Also, as I learn and evolve the layout, some of my wiring methods improve and change, so that is all described in the xls file.
I also have troubleshooting notes, which I am always adding to. It is unbelievable how many things can go wrong on my layout. The layout is idle during the summer, so come the fall, many things do not work, for no reason whatsoever. It does not make sense, it is simply an observation of the facts.