You can now create folders (Collections) in iBooks 1.2. Unfortunately, it's only within the iBooks app, and not in the iTunes interface. Press the Collections button to create new folders and then press the Edit button to select and move the books or PDFs into the collection. You can also create new Collections in the Edit mode after you've selected at least one book or PDF and then press the Move button. Swiping the Collection of Books left or right moves through the Collections.