I'll join taylorkh in that I'm not sure this would be possible. Since I think that in that case every client would need to implement SSL, or run the ssl proxy. Not feasible.
The best I know of that comes close to your requirements is bittorrent encryption. Most known clients should support this (KTorrent, rtorrent and µtorrent do...). Not sure how it works internally, but a basic description is on
wikipedia
Serafean