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1. Calibre accepts both ePub (provided it's DRM free) and Mobi. You can add them as they are, you have no need to reformat.
2. Except for PDF and DRM'd books, you're probably going to use FBReader. FB2 has an advantage as it's the native format for the software, but one can read ePub, Mobis, Docs and the like and there are no issues to come. Beware of converting PDF's to other formats with Calibre though, as the output tends to be harsh on the eyes.
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