Calibre requires X or graphical frontend, even for it's command line tools such as ebook-convert!
Kindlegen will have no problems working in command line only environments. (ie. server environments)
Calibre, as of 09/2011, produces better viewer (formatted) output vs. kindlegen for complex HTML files using <TABLE> tags. If you're only converting simple HTML pages (ie. without <TABLE> tags such as using man2html), then formating these simple HTML pages to .mobi with kindlegen will be just fine and, if not, identical to Calibre.
See AmazonKindlePublishingGuidelines.pdf for specifics on supported tags and formating of .mobi books.
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http://kindlegen.s3.amazonaws.com/Am...Guidelines.pdf)
(This is posted for historical purposes and those searching.)