Probably way off base, but here goes...
If you want to save the contents of a web page into a reading friendly format, then there's Instapaper (4.99). Great app, but not sure if that's what you want. It can organize into folders as well.
GoodReader is another app that can organize documents into folders, along with images, etc and sync with cloud (0.99).
Neither of those can take notes. If you're looking for all that in one app, then I'm at a loss.