According to some leaked screenshots and descriptions, Apple's iBooks app for iPad, iPod touch, and iPhone will be getting an update in the near future that includes "collections", along with PDF printing and emailing.
Collections are similar to folders. You will be able to make groups of books and PDF's that are accessible via the new "collections" button as well as from your bookshelf. User-created collections are completely customizable, but the the two default collections, Books and PDF's, are not.