As promised, tips and tricks for managing libraries of unprotected books...
(Note: Personally speaking, I have no ethical problem with removing DRM for strictly personal use. In fact, doing so makes things much simpler, because you don't have to deal with maintaining the DRM connection across multiple devices; they become unprotected books that you can use the following tips on. It also lets you do things like edit titles, such as to change "The Two Towers" to "LOTR 2: The Two Towers" to make series order more obvious. However, this practice is illegal, therefore I can neither endorse the practice nor mention software that might facilitate it.)
The great thing about EPUBs - which are what Kobos use - is that they're basically web pages in a ZIP file, just with a few extra files and a new extension. This means that, if you dislike something about an EPUB, it's probably not hard to change it. I mentioned changing titles; that's as simple as editing the *.opf file in the archive, which is a pretty straightforward XML file that you can edit as text. (I use WinRAR to open the book as an archive, and I have it set up to use Notepad++ to edit the internal files when I double-click them.)
Even if you don't do any internal tinkering, you can still organize your books reasonably well. I keep a "copied to X" folder on my hard drive for every distinct destination, devices and cards alike. This basic step creates a backup; in essence, I "check the book out" of the library by moving it to the "copied to X" folder, and then I "return" it by deleting it from the device and moving it from the "copied to X" folder back into the main library. The point is that
anything not on the hard drive is deemed ephemeral and disposable. If I lose my reader, it's only a financial hassle to replace the hardware. Restoring the books is just a question of recopying the "copied to X" folders.
I buy a lot of series books, and I name them with a mnemonic for the series, the number of this volume, and the main title of the book. Hence, "LOTR2 - The Two Towers.epub" condenses a lot of information into a little space. I then file those books inside their own folder, which may go into an author folder. That, in turn, goes into a genre folder. Thus:
(prefix)\Fantasy\Tolkien\Lord of the Rings\LOTR2 - The Two Towers.epub
For standalone books, I generally put the author's name where the series code would go:
(prefix)\SF\Robert J Sawyer\Calculating God.epub
That hierarchy works for me, but use whatever works for
you. Who cares if your system works for anyone else, right?
Anyway, that same basic structure carries over into all of the "copied to" folders (and thus those destinations), in addition to the core "Finished" and "Unread" folders. When I buy an unprotected book, I download it to the computer into a "Pending" folder, process it as desired, connect either the reader or the card, copy the processed book(s) to their proper places there, then move them to their proper "copied to" folder.
The big advantage of this approach is that it's easy to find a given book. It's also easy to back up the whole library. All I have to do is make a new folder ("Ebooks 7-18-2013"), copy Copied to Kobo\*.* into it, then repeat the process with every other library segment. Since the hierarchies are all the same, they'll all merge together into one complete backup. Even easier, I could maintain the separation and just back up the master folder (which contains all the segments) as a unit.
Obviously, DRM throws a big ol' monkey wrench into that whole scheme. About the best I can do there is copy all the DRM'd books into a clearly-labeled "Adobe DRM" folder (since that's the only form I use) and either (a) make a cheat sheet pairing the arcane names of those books with their actual names or (b) hope I can decipher them later. Neither option is really good, which leads me to prefer books without DRM.
At least I do know that if I
move books from the actual ADE folder into that backup folder, that gets them out of the way there - and I can copy them back later if I need to. Yeah, I
could apply the detailed hierarchy to those files, but how useful is that really going to be?