You can import entire folders into Calibre. I think MobiPocket's default folder is My Documents\My eBooks (it can be changed, and I use My Documents\My eBooks\Mobipocket). The K4PC ebooks are in My Documents\My Kindle Content. I don't know where eReader ebooks go, but they are most likely in some other folder in My Documents.
For all three formats, you can add plugins to Calibre to strip the DRM (if any) during import. See the tools_2.4 bundle, and as usual Apprentice Alf's Blog is the place to go for DRM info.
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