Apps may be the future for many encylopedia style books and young children's books where video, animation and sound can be just as important as the text.
For fiction books aimed at young adult and beyond though I see apps being nothing more than a novelty (famous last words I guess
). There might be a market for buying a special edition of an ebook as a bundle that includes the standard ebook mobi/epub form + a download of the enhanced app.
For example, LOTR or HP would never be replaced by an App. I really cannot see it. However, I could see in addition to the ebooks an "Everything you wanted to know about LOTR/HP" style interactive book that would include maps you can zoom in on, click on an area to bring up information about the region and links to clips from the films that took part there. Cast interviews, behind the scenes clips and interactive games.
So in a way apps are the future of some books but I think it'll be more of a symbiotic relationship with traditional ebooks.