I use a spreadsheet (open office). I keep several different files. I have one master file for everything. I then have files that are separated by interest, public safety, business, marine, rail etc. My military air stuff is also kept in a master list but I also have separate lists for SATCOM, different modes and the different bands and such.
I have lists done for each of my radios too detailing their memories and search bank contents. This is especially helpful as many of my radios do not have computer control. I print out all the channel and search bank data, place it in plastic sheet protectors and assemble them in 3 ring view binders. I customize these for each radio. The “view” binders have clear pockets on the outside and spine which allow you to create a custom spine and covers for them. It is nice to be able to look over and see a freq on the radio and quickly grab a binder on a shelf, flip to a page and ID a freq. It is faster than booting up the computer and typing it into the search box. Even if it's already up it's even faster than doing the series of mouse clicks and opening up the file and searching for the freq in the file. Sometimes the old ways work.
By the way, the view binder thing works good for manuals too. Most manuals come on PDF now. Many scanners and receivers are getting to be awfully complex and you're constantly having to refer to the manual and they can get pretty dog eared. Some of those manuals can get kind of expensive to replace. I print out the PDF, place the sheets in plastic sheet protectors and assemble the whole works in a view binder. The cover usually prints off and the whole thing looks pretty sharp when you're done and it can be identified on your shelf pretty easily. It protects your expensive paper version and is nicer to work with as you can mark the chapters with tabs, make the print larger, highlight sections and customize it as you like.