Our bookshelf has folders, sorting, user defined tags, custom file filtering, cutting copying pasting deleting of files, more.
We have two different reader programs, FBReader and Coolreader (you can use the one you prefer), that allow full customizability of reader experience, with features such as: margin, line spacing, precise font size settings, custom user fonts, dictionary, text search, etc. etc. etc. As well as support for just about every book type you can think of: fb2, HTML, CHM, plucker, Palmdoc, zTxt, TCR , RTF, OEB, OpenReader, mobipocket, text, and more.
Our PDF reader supports white space/margin trimming and full panning and zooming.
This is just off the top of my head. There are lots of features not listed.
When it comes down to it, the most important thing to me is that I can make my books look EXACTLY - to the pixel - the way I want them to. No other firmware lets me do that. I got involved in this project, essentially, because of pathological pickiness.
Our port to the cybook is very far along, but stalled because we don't have any developers working on it (we are in the process of porting to some other devices and have no time). Find us an interested developer with a cybook and some time on his hands and you'll have your folders, and a whole lot more.