I gave up on Collections. I load books onto my Reader from three different computers, one of which doesn't have Calibre installed. (I can sort-of run it portably on my flash drive, but it's troublesome that way.)
I sort the books in folders that I can only see when I'm connected to a computer, and just deal with scrolling through the lists to find the ones I want. Since I have a lot of homemade PDFs, I often put a prefix in the title metadata to group them when I'm sorting by title.
I'm considering switching to the Aztak Pocket reader to get folder support. (Only considering, 'cos that's a lot of money to invest in replacing a device that's working very well for me now. I expected to get 2-3 years out of my Sony Reader; right now I've got less than 1 year with it.)
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