The paper-based book or e-book can be arranged so reading from cover to cover gradually educates the reader in the order the author feels is most effective.
The wikis I've typically seen tend to be more like a reference manual. You read a page and then it's back to the table of contents to choose another topic. They seem to lose that incremental learning approach books can rely on.
Wikis have the advantage of being kept easily up-to-date; no waiting for second edition or the release of a new PDF.
Blogs are nice in that the readers can ask for clarification of the article just read, but they tend to be a collection of random thoughts—again no structured learning path. Ideally it would be nice that a reader could click on a sentence they wanted to comment on and attach one right there.
I'm not having much luck searching and suspect I'm just missing that key phrase that anyone using such a thing knows instantly, like "authoring framework" or something.
Update: I've found something just about spot on here based on DocBook markup but the platform has been written by the author. See how it reads more like a book than a wiki and readers can leave comments on each paragraph.
He makes the platform freely available which is great, but it would still be good to know if there's a name for this sort of live, commentable ebook format.
update 2: Amazon ebooks allow commenting and highlighting, which anyone with (the ebook and) a kindle or kindle app can turn on public comments and highlights (ln the settings) to view them.