Even for reference materials, ebooks still seem like the bastard child of a reference textbook and a proper hyperlinked manual.
For novels the difference (for me at least) is that the Kindle makes it easier to focus on actually reading.
I was surprised by this but turning a page is a small nudge of the thumb and your focus remains on the text, the device is light enough that holding it in the same position for an extended period or getting comfortable in bed or in a chair is far easier than for a book (even a paperback - and the difference between the Kindle and a hardback or trade paperback isn't even funny). Small barriers that you weren't even really aware of that are either taken away or noticeably reduced.
Of course there's all the additional stuff - buying books instantly nearly anywhere, carrying a whole library in your pocket and so on - but they turn out to be bells and whistles. The real difference is that it's just a better device for consuming text.
For reference books (at least large ones) the Kindle isn't there yet (layout, searching, colour and a few other key things) but without having hands on experience I can see the iPad could well remove most of those issues at which point searching and electronic notes, combined with reduced bulk (the iPad is heavy but not next to a 500 page programming book) likely give it an edge over paper.
Then again, I don't know how to write a love note on the front page of ebooks I'm giving as gift, and they are still not bathtub-compliant :)
I also find navigating a book-length document on a laptop or something quite tedious. When I'm reading a complex book (where I often want to refer to the index, endnotes, or photographs) I will often have several fingers folded in at the relevant pages and can jump around quite quickly.
Introducing a playback device (such as going from book -> Kindle + ebook) is quite different, I think.
Also, there's definitely something to be said not only for carrying your book around on a light device, but carrying up to thousands of them around on a single light device. (Though, on the other hand, how often are you going to need to go back and read most of your non-reference books after you've finished them?).
As a book nerd, you often relate to books in response to certain situations. Instead of summarizing, we can now quickly access the eloquent prose of a gifted author that had time to express herself :)
I think eBooks are fine for "on-the-go," but hard copies certainly have a place on my bookshelf. In time, hard copies will become a niche product, one you use while sitting in your easy chair on a cold winter night. Everyone thought the radio will die with the advent of TV, but it just found a niche (nobody listens to the radio in their house, but they do in their car).
As a side note, the OP said that he prefers reference books as hard copy books. When I think of reference books though, I think searchable content, which means I want my references to be in eBook format.
Paper books still have some interface advantages over ebooks (as several people have described in this thread) but they'll go away as people build proper, well designed ebook readers.
When that happens, all books will have going for them is nostalgia and a pleasant physical experience that can't be replicated digitally. I think a much more apt comparison is records, which don't provide a fundamentally different sonic experience, but do have nostalgia and physicality.
So I think a handful of book lovers will still have collections, and visit the bookstore down the street, but like record players, and unlike radios, I think the vast majority of the population won't have any.
Definitly. There's something exhilerating about bringing all your books with you.
There are practical advantages aswell. I'm going on a 3 week holiday to australia soon. Previously I'd have to deciede what books I want to bring with me (since I couldn't take them all). Now I don't have to think about it. I just take my kindle and I know I have all my books.