When I tried freenet it was so slow that it would compare unfavorably to a website being DDOSed, so that's perhaps a bad example. As far as bittorrent goes, it is entirely possible to DDOS the distribution of the contents of a single .torrent: DDOS every computer seeding it. Might take more effort than DDOSing a commercial site, or it might not, depending on how much downstream the seeds have.
Some protocols are immune to DDOS: like BitTorrent and Freenet. HTTP wasn't designed to deal with DDOS.