Pandoc will help you convert documents between various markup formats. You can input documents written in either Markdown, HTML, or LaTeX formats and the tool will let you convert them into HTML, MediaWiki, LaTeX, DocBook, Markdown, and RTF formats.
Pandoc can also output documents in EPUB format which is compatible with iPads, and other ebook readers. There’s also support for LaTeX math, tables, and footnotes.
You can either use Pandoc online or they offer installer binaries for Windows, Mac and Linux. It’s a command line conversion tool with no GUI though.