So, I've been following this discussion with interest. I'm still confused. All I'm really getting out of the comments on this thread is: there's some other objects in the system that aren't DAOs or entities. But I knew that already. Clearly, I need to actually read the damn book for myself. Still, it really doesn't fill me with confidence that people who /have/ read the book don't seem to be able to explain (in words or code) the Repository notion coherently. And it looks like everyone has their own private take on what exactly a Repository is all about. This gives me a hint that the idea is not especially well-defined.
I've recently read the book Domain Driven Design, which apparently is now the new bible for some folks who totally think in objects. I even mentioned it in HiA and JPwH - unfortunately I didn't read it before.
Kinda tangentially related to this discussion, I'm often asked whether I believe in rich domain models or anemic domain models. I guess I'm pretty much ignorant as to what these terms really mean, since I've never seen a proper definition of either term.