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Hi there. Amazon's Kindle software runs on not only the Mac, but also the iPhone, iPod, and iPod touch (and I assume on Windows and Android), as well as on a Kindle device. The ebooks you buy from Amazon are available in your Amazon "digital locker" and can be transferred between any copies of the software that you have, so they can move to your iPad and your Kindle, or you can read them on your Mac, or any combination. Those files are (basically) in the Mobipocket format.
There are three common ebook formats right now: Mobipocket, EPUB, and PDF. Some vendors (like Take Control) make their ebooks available in all three of those formats. Some stick to just one (or two) of the formats. So, Amazon and the Kindle is Mobipocket only. For another example, Apple sells only EPUBs in the iBookstore, but Apple's iBooks app on the iPad (or iPhone or iPod touch) can read EPUBs and PDFs, but not Mobipockets. The iBooks app is only for iOS devices; Apple hasn't released it for the Mac or for any other type of device.
As for Bookle, it runs only on the Macintosh. And, it reads only EPUBs that do not have Digital Rights Management applied to them.
I hope that helps... there's a lot of going on right now with all the different formats, applications, and ebook publishers, and it can be a lot to keep track of.