ShowHN: Using SSH for file sharing among users (Python Project on github)
divinequantum.blogspot.in
divinequantum.blogspot.in
If they have shell access, why not simply use scp or rsync?
You can run the hub on any port you like to circumvent the first (let's see them try and block port 80!), and use an ADCS server to circumvent the second - still compatible with DC++ and recent mods (ApexDC, StrongDC et al)
You might also want to look into DTella to decentralise your network.
EDIT: As a solution that doesn't need apps and uses the server only as a temporary middleman instead of actually storing the file, there's JetBytes[2].
[1]: http://www.getshareapp.com/
[2]: http://jetbytes.com/
But one problem is still remaining, and the present solutions are under the heaviest attack: discovery. BitTorrent is using trackers, and we've seen attacks on sites like PirateBay that provide those services. Is there a way to develop -- or perhaps it's been done already -- a discovery and tracking system which is truly P2P and simply cannot be attacked, at least not in a technical way?