Just to make sure we’re on the same page (pun intended), footnotes are citations at the bottom of pages; chapter endnotes are citations at the end of each chapter; and book endnotes are citations compiled at the end of the book, usually prior to the bibliography.
Personally, I love footnotes. Being able to glance down at the bottom of the page I’m reading to check a source or read an explanation for an argument is convenient.
I’m not particularly fond of either type of endnotes. The one advantage of chapter endnotes over book endnotes is that they are easier when it comes to photocopying–you don’t have to photocopy a chapter, then flip to the end of the book to find the relevant pages in the book endnotes.
Publishers seem to be moving toward book endnotes. I’m not sure if book endnotes are easier to handle in terms of production or if they make the book shorter and thus cheaper in price. Maybe someone in the industry can enlighten me.
Poll result update (27 April 2012): Footnotes, 20 votes; chapter endnotes, 2; book endnotes, 0.
Jacksonian America: Society, Personality, and Politics 
Thank you for raising this. I’m a writer with more than 20 books out, and I’ve always wanted my footnotes at the bottom of the page, but the publishers haven’t wanted this. One publisher early in my career jokingly said, “I would see you dead before I’d allow you to do that to yourself.” Once again, a joke, not a threat. But it reveals how much he hated footnotes at the bottom of the page. I’ve never understood that. I vastly prefer footnotes where I can look at them as I read. Especially for explanatory footnotes. I am starting this discussion right now with my current publisher. I hope he lets me put them at the bottom of the page, but I doubt he will.
Unfortunately, footnotes are going the way of the dinosaur. None of the books I’ve written/edited since my first one have had them, and none of the ones I’m writing/under contract for will have them. It’s a shame.
I prefer footnotes by far, followed by chapter endnotes, with book endnotes being better than no notes at all.
I’ve seen the suggestion that publishers think notes scare off potential book buyers. Whether that is actually a rationale by publishers, I don’t know.
I can see why notes would be troublesome for trade publishers but not university presses. That’s a good question for one of the panels/roundtables that editors sometimes participate in at the AHA/OAH.
I go back and forth between prefering footnotes or chapter endnotes. I hate end-of-the-book endnotes because I have to keep flipping back and forth to refer to one as I read the text. Footnotes are great for research, but they can also be a distraction if I’m reading for pleasure. As a book designer, I’ve compromised by using chapter endnotes.
You’re a good person to ask. For publishers, is there a difference between footnotes and endnotes in terms of production cost?
For me, it’s not as much a matter of the production cost as it is the aesthetics of the printed page. The inconsistency of footnotes–some more lengthy than others–leads to an inconsistent block of text on the page. For instance, the left hand page may have more narrative than the right side. For the last two books I’ve designed, I compromised by using chapter endnotes. They’re not as far away from the chapter to which they refer and don’t distract the reader or draw him/her away from the narrative. But for research, I prefer the handy footnotes for easy reference. It’s a constant struggle! I’d be interested in what your readers think about the issue for my own standpoint as a publisher.