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When you say 'different formats' are you speaking about different formats for different readers (Sony, Mobipocket, Microsoft Reader, Iliad, Kindle, etc.) or do you mean different formats as in LRF, PDF, RTF, etc. all for reading on the Sony Reader?
If they're all for reading on the sony, then Calibre would be my suggestion.
If they're for reading on different machines, then I don't know if there is any program other than sorting things into different folders manually using Windows Explorer (or some other similar program such as Z-tree which makes selecting and moving files much easier than Windows Explorer.)
If you on a Mac, I have no idea what to suggest.
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