I'm sure that this is blindingly obvious to everyone else, and I'm just slow, but...
... I've just discovered that you can rearrange your books on the iBooks "bookshelf" by clicking the "Edit" button at the top left, and then dragging the books around into whatever order you wish. This is great for getting the books in a series into the proper order, for example.
As I say, doubtless everyone except me already knew this
.