Update: So much for rumors. Readers have let us know about two German websites pointing to explicit discussion of iBooks collections in the iOS 4.2 documentation, of all places. We can expect to see collection support in the next version of the iBooks app, which can be updated independently of the main OS releases.
Steve himself has hinted at improvements "coming" soon to iBooks, and 9to5Mac claims to have nabbed some internal Apple documents that lay out those improvements. The biggest feature is called "Collections," and it sounds like it works the same as Folders in the rest of iOS -- you can combine items in iBooks however you like, and the collections you've got in iBooks can be viewed right on your bookshelf in the main screen. Sounds handy, if not all that revolutionary.
Second, PDF users will get some nice additions -- PDFs will be able to be shared via email as well as printed off with AirPrint directly from the iBooks app. That functionality won't work for actual book files, obviously, given that if you want to read one of those, you'll have to buy it. But if this document is legit, it should make things a little easier for people who want to share and print PDFs from iBooks itself.
We don't know yet when these features will actually come to iBooks, but presumably we wouldn't need to wait until an iOS update -- Apple could update the iBooks app. We'll keep an eye out for that soon.