EPUB and MOBI are very popular e-book formats for handheld devices. Helpinator creates EPUB files directly, but to compile documentation in MOBI format you will need Amazon’s KindleGen command line tool and Kindle Previewer to see how your documentation will look like on Kindle.
To download KindleGen click here: http://www.amazon.com/gp/feature.html?docId=1000234621
To download Kindle Previewer click this link: http://www.amazon.com/gp/feature.html/?docId=1000765261
KindleGen comes in ZIP archive so you will have to unzip it, Kindle Previewer comes with installer.
Once you have KindleGen unzipped, run Helpinator, select Main Menu->Tools->Options, “Compilers” tab and path to the KindleGen folder into the “MOBI” field.