With the latest version of iBooks for Apple's iOS7 comes the total disappearance of the 'look of the book'. No more pseudo leather look cover or page edges; no more shaded spine, nor even the wooden bookcase for your library.
Apple's decision to do this falls in to line with the re-design of iOS - making for a much simpler (minimalist - you might say) look and feel. Much of the shine and shadows on any icons and objects has gone.
When it comes to the iBooks app, there are some issues that need addressing and I am disappointed that publishers have lost some element of control. Strange things happen when you compare re-flowable with fixed layout though!
Update: As of IOS 9 and iBooks 4, I don't recommend that you try to get non-linear content to work. You will be able to use the popup as described below here, but the display on iBooks for MAC is not good; you will find that the height of the popup will fill the screen. Even if you have an html document set (in the spine) to be 'non-linear' iBooks 4 will show the page when the reader reaches that point in the book.
Being able to link to content within an eBook package but not have that content navigable by any other means is a very useful feature supported in re-flowable eBooks within the iBooks app on Apple iOS devices.
In my book on eBook Typography for Flowable eBooks, I demonstrate this feature for tables, scrolling text and even PDFs. Unfortunately, it was not possible to use this feature in fixed-layout ePub eBooks destined for the iBooks app.
Or so I thought! I have recently discovered that the latest version of the iBooks app on iOS7 does support it even though, Apple's own documentation says that it does not!
Edit:See below - it does work on earlier versions of iBooks /iOS