PDF is definitly the way to go and offers a wide variety in terms of security. Yet please have a look at issues that go along with that. DRM is definitly an issue that needs to be considered. Otherwise you’ll find your work spread around the globe and have officially sold two-and-a-half copies. 
Most books or articles I read are at the airport or in my backyard on my handheld. And PDF really sucks for that. Another issue in that context is that I don’t want to be having my notebook around with me everywhere. Making the book available as a combination of both mobipocket and PDF (whilst compressing it into a ZIP for download) would probably give you a big gain on and impress mobile users. 
I hope I was able to help you out. If you have further questions please feel free to contact me. 

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