The iBooks app? I've certainly added plenty of my own epub's and PDF's to it.
Yes, it lo longer works via iTunes as it used to. I have found you can drag and drop epubs over to the phone/iPad, but you can no longer sort or select via iTunes as you did before, it has to be done on the device. This is a total mess, especially dealing with versions of books as every device has to be updated separately (Some of my books might be updated 3 or 4 times over a semester)