The only thing I feel that is actually inherent to the net is the hyperlink. Which is useful in letting information, references, or otherwise sit closer to the text than a footnote; but then can be often used in the place of explanation, thought, or perspective.
Though as one tech writer said at a talk a few days ago, ‘clicking is through, it’s all about scrolling now.’ Which as a writer hasn’t impacted things much yet (I don’t think Triple Canopy’s sideways scroll constitutes much of a shift, though it’s good and more things like this should exist). This will keep changing, say with web design incorporating users’ movement into a pseudo-interactive proto-cinematic/animation motion: http://feature.rollingstone.com/feature/the-geeks-on-the-frontlines, but how that effects writing I’m not sure – part of me thinks it’s just like showy open credits animation, and the business of writing and reading will still requite stability for transmission.