I’ve had this idea of designing a new tool/interface for reading/working with scientific papers some months ago…
On the left, big part of the screen, one would have the actual paper and on the right there would be several boxes with different kinds of resources, e.g. the papers referenced in the text as hyperlinked PDF documents; multi-media illustrative material, like movies, photos or sounds, also hyperlinked from the text where needed; user-generated comments and notes, also hyperlinked to the parts of the text they related to.
I will try to make a drawing of this interface as soon as possible… 🙂