Azureus and uTorrent (the two most popular bittorrent clients) had included in their latest beta new forms of encryption, which will provide a completely random-looking header and (optionally) payload to avoid passive protocol identification and traffic shaping. The technical details are a bit hairy, but if have the guts you can always take a peek here.

But Bram Cohen, the guy who invented the Bittorrent protocol, does not agree with this decision, since he believes that ISP's will be able to still detect Bittorrent traffic, and that this could harms the Internet performance as a whole, as stated in his blog.

What's next, an encrypted Skype?