i find ibook's organization to basically be lacking. here's what you can do:
1. bookshelf view. where you're looking at covers (if the book file has a cover graphic embedded, if not you see a generic cover with the title). you can't sort but category, title, etc. in this view. the book covers are displayed on an ever growing high bookshelf. what you can do in this view is hit the edit button (upper right) and manage your books similar to how you manage apps. a X circle appears in the upper left corner of a cover, if you tap it you'll delete the book from your ipad. if you press and hold in the middle of a book cover it zooms out a little, and you can drag and drop it to a new location on the bookshelf. so you can put your favorites or current reads up top and everything else eventually sorts to the bottom.
that's it for book shelf view.
2. there is a list view. going into this gives you a long list, with a small cover graphic on the left, followed by the title in bold text with the author beneath it in a smaller font with grey text. to the far right is a column with the tags of the book from itunes. whatever is in the "genre" field in itunes.
below the list are four buttons. the first is "bookshelf" which i guess lists the books in the order displayed in the bookshelf. next is "titles" which sorts by title, alphabetically (and if you want, you can edit the books info in itunes and change the sort title, look around and you'll find it). "authors" which sorts by the author's last name. and "categories" which sorts by the "genre" tag.
there's also an edit button in this view as well which allows a few different things. in "bookshelf" view you can delete as well as re-order books (which will be reflected if you go back to the book shelf view). in titles, authors or categories view, you can only delete the books, you can't re-order them in any way.
a few extra notes.
1. you can't edit any of this information on the ipad itself, but you can in itunes, changing the title, author, genre, etc.
2. the genre/category tag only takes one value. so you can mark a book as fiction or fantasy, but not "fantasy, fiction" like you might do in calibre. the genre tag is a free form list, but it's also shared with your movies and music as well.
3. there are no nested categories or folders or extra bookshelves or anything to help you group up books, other than the category/genre tag. it's too bad you can't scroll left/right to get a new bookshelf (in a different color would be nice) and put different books on different shelves. maybe ibooks 2.0.
4. there's no way to loan out a book, like the nook. but all ipads that are synced to a particular computer can load up any books associated with that itunes account.
personally, i don't care much for the ibook app at this point. but i was spoiled with stanza and my sony 600. it's not bad for a 1.0, but it could use some more features. i think part of the problem is itunes (which was born out of soundjam) was developed for organizing music, not books. apple really needs to add in better organization that makes sense to each media type.