The Kindle can link to a Linux machine and you can manage and sync it with
Calibre which is in the repositories. Calibre can convert most formats, but
does not handle the AZW or TPZ file formats. It can work with: CHM, LRF,
PDF, LIT, RTF, OPF, MOBI, PRC, EPUB, FB2, IMP, RB, HTML. However, if you
have a book in a format that you can't handle such as EPUB then you can
convert it to PDF which newer Kindles can handle or MOBI which all Kindles
can read. You can also use the Amazon service for some conversions.

Check out the Calibre website for more info:
http://calibre-ebook.com/user_manual/faq.html