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ePub. It's basically zipped-up HTML files, and an officially open standard. Very easy to make and modify, also easy to convert to just about anything else you might need. Available on an increasing number of platforms, too.
Mobi may be more common because of Amazon's market dominance, but it's a closed format (I think that most open-source implementations are based upon "best guess" reverse-engineering) and every time you want to change something, you'll basically have to unpack, edit, and re-generate the Mobi file again and again.
It's perfectly okay for reading, but not so great for creating. And I say that as a Kindle user who automatically grabs the ePub file if it's available over the Mobi file if I'm given an either/or choice between the two.
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