Aside from the usual tags for genre, etc., I have a bunch of utility tags:
[processed] for the ones that I've gone over, fixed the metadata, found the cover, etc.
[main] for the ones that go to the Reader's main memory.
[card] for the ones that go to the SD card.
[DNU] for the ones that don't go to the Reader at all (primarily huge PDFs with teensy print).
[paid] for non-free books, so I don't accidentally mix one in with the Baen Free Library or something.
My most important saved search is the "NEW" one, which is just every book that doesn't have a [processed] tag. I import a bunch of books, pick that search, and I can then go through and work on all of them at once: fix their missing metadata, search for a cover, tag them by subject, etc. Once I'm satisfied with the metadata, I give that book a [processed] tag and it goes away, into the great sea of To-Be-Read.
I'm seriously thinking of adding a couple of reading priority tags: "read now" and "read soon". I'm constantly finding something neat somewhere like Project Gutenberg, tossing it on the Reader to read later, and forgetting about it.
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