It depends on the book, really. I still use my old Kindle and have a limited amount of space on it. So anything that's not an old favourite or part of a series that I'll probably want to skim through again once a newer installment comes out tends to go when I do the periodic purge. Same as for the comics on my BlackBerry PlayBook, even though I've got more space on that (but comics files are much larger, and too many of them in the library seems to make the none-too-stable ported reading apps crash).
OTOH, I have an 8 GB card in my Sony, so I guess technically it would be a long time before I filled it up. But in practice I tend to delete and reload a couple of times a year.
As for organizing my ebooks on the Mac, I just use the built-in Finder tags (and I suppose I could be using the comments and versioning as well). All I really keep track of is author/title/translator/original title/series #/year, which I can do in the folder names, and whether or not I've read something, which I can mark with coloured tags, so my needs are pretty simple and this is something that works well enough for me.
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