iBooks vs epub: What's the difference? Until now, I was under the impression that ePub was the de facto standard for Apple and the default format used by iBooks. But recently I downloaded some ebooks from the iTunes store and found them to have the .ibooks extension instead. What's the difference between the two? Also, how can one convert an ePub document into an ibooks document, if that is possible?
.ibooks files are a special Apple-only multi-touch version of the epub standard.  They can only be created using the iBooks Author app, and they can only be read by the iBooks app on an iOS device or a Mac running OS 10.9 or higher. 

The main attraction of the .ibooks format for authors is that it can easily incorporate a large variety of interactive features via widgets.  The Apple list is at http://support.apple.com/kb/PH2789 and a 3rd party list is at https://bookry.com/author/widget/library/

.epub is an open standard which can be produced by a number of apps (including Apple's Pages) and can be read on any platform using a variety of apps (including Apple's iBooks).  There is no way to convert .epub to .ibooks, other than to put the content into iBooks Author and republish it from that app.

Starting with version 2.3 of June 2015, iBooks Author can also produce .epub format, as long as one of the .epub templates is used.