I haven't managed to fill up an eink reader yet. Perhaps I might have filled my first Cybook Gen3, but I had a 2G SD card to put into it so never worried. With my Pocketbook 360 Plus I haven't bothered with the SD card as there is so much room available 'on board'. I own over 1000 ebooks and all but those I've read in the last 2 years on on it. So, at least 900 ebooks are loaded.
I can easily find any book I am looking for as I have a folder for each Genre and have named each file in this format: "Author_Series00_Title" or "Author_Title" if no series. This way as long as I know who the author is I can get to the next book in the series or the next book on my TBR list.
I've been using this system since 2007 and it seems to be working so far. Before folders were an option I added "Genre" to the beginning of the file name. That did make for a lot of 'page turns' finding the next book on my Gen3, but it was worth it to have my whole 'library' with me. I tend to read a LOT and like to be able to change books on a whim, reading several books at a time, so dedicated readers have been great for me!