Here's an entry outlining YouTube's new approach to infringing content:
http://valleywag.com/390528/how-youtubes-sucking-up-to-modest-mouse-and-...
Some of its mechanisms include removing the embed codes from the infringing page, and directing users to the copyright owner's own version of the work.
It's unclear as to the level of sophistication of YouTube's fingerprinting capabilities, though the article suggests they're working with Audible Magic:
http://www.audiblemagic.com/index.asp