Other than Amazon's proprietary Kindle environment, virtually all eReaders (B&N 
Nook, Kobo, Sony etc.) and virtually all eBook clients and apps (Apple 
iPad/iPhone/iPod Touch iBooks, Android Aldiko, etc.) are standardized on the 
open epub and pdf formats.

As John previously remarked, pdf format is less than optimal, especially on 
smaller screen devices, since page formats are "locked". Epub allows for 
reading software to reflow pages so the books/manuals appear optimized for 
whatever device the book is displayed on.

Mobi format is an old format that's still of some importance because of 
compatibility with older devices and software. Leading modern eBook products 
(i.e. iBooks, Aldiko) do not support mobi.

If you're looking into publishing manuals in eBook formats, especially with 
portable readers in mind, I recommend you take a look at Calibre. This open 
source project has become the de facto library management and ebook conversion 
software of choice for those who have needs beyond a single commercial ebook 
store.
The project is located at caliber-ebook.com.

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