In the latest progression of the FCC versus Comcast, the former has officially ruled that Comast was in the wrong when they decided to throttle BitTorent traffic and acted illegally in doing so. Furthermore, the FCC has ordered Comcast to cease filtering traffic, saying they must use only "protocol-agnostic" means of controlling bandwidth.
The FCC has challenges getting such orders enforced, as currently they do not have any ability to actually prevent or fine Comcast for doing such. However, the ruling does send a very powerful message to Comcast and many ISPs, as well as set the tone for future battles between ISPs and their customers. Comcast will likely appeal the ruling. Even if they do appeal and manage to get the order overturned, they have already lost considerable face in the public eye and it is unlikely they will revert to throttling based on application again.