eBook formats - Kindle to iBook and back?
Note that there are now three main eBook formats   


PDF which is not reflowable text and is used mainly for graphical books. There is a open specification for this.
MobiPocket(Kindle files with extension .mobi (and encrypted as .azw)) The specification is not published and so Amazon can change it when they want.
ePub which is most of the rest including iBooks. This is a published specification and there are open source tools that can create, edit and validate that the book meets the specification.


If the books do not have Digital Rights Management(DRM) then Kindle books can easily be converted to ePub as the format is similar, the reverse can also be done but you might lose some information as ePub data contains more things than Kindle data.

The easiest way to convert is to use Calibre which is a tool for managing ebooks including conversion, loading to devices and organisation of a library of books.

DRM books are tied to the application with which you bought them. An exception is that many ePub EBooks (but not iBooks and not Kindle) use Adobe's DRM and so can can be used in several devices.

There are plugins to Calibre, which are not legal in many countries, which allow removal of the DRM and thus use in Calibre allowing conversion between the formats. However I belive that there is no plugin for decryption of iBooks files.