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A good app for viewing and managing files is Goodreader. One advantage it has is that it integrates with Dropbox, which is what I use for transferring files to and from my PC. Another tip is that I Books organizes files by collections, one for regular ePub books and another for PDFs.You can stash all your PDFs in iBooks.Evernote is my preferred note taker and organizer. You can use DRagon Dictate to do voice notes, but I really haven't used that much yet.
I have found that between Goodreader, Dropbox, and IBooks, I can achieve basic file management tasks. I'm hoping Ios5 brings better file management to the IPad.
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