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Personally I have had nothing but bad experiences with Caliber. It took forever to add books, and it made a total hash of my folder where I had been storing my library.
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Ditto for that. I'm on a Mac and keep all my books on a NAS -- Calibre won't connect to the remote drive and even if it did it copies the books to its own space rather than using my existing archive. Plus its really, really slow.
For me on a Mac:
Stanza to convert formats.
Hidden Cleaner for Mac -- freeware that cleanly unmounts the device. The jetBook loves to leave trash folders behind :P.
The Unarchiver for uncompressing things.
TextWrangler, Bean or NeoOffice for text cleanup.
A multi-disk mirrored or striped NAS for redundant long term archiving.
Memeo Backup -- automatically copies files up to the NAS.
I've yet to find a sync tool for the Mac/Linux I'm happy with
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