I do it all by file folders. On the PC, it's ordered by broad category then author; on the device it's the dozen or so things I want to read next, plus some common references, plus an SD card of "you never know" reference books like first-aid guides, in case there's a zombie apocalypse or something.
Management software all seems to put an annoying layer between me and the file folders -- I'm the same with music on my MP3, so I expect this is more to do with me than it reflects the software.
Storage capacity's only challenged when PDFs or manga get involved.