I posted a video on YouTube (SFW) nearly two years ago, with an ambient soundtrack taken from an Aphex Twin song (which I credited at the end of the video). After nearly 3000 views, it has had the audio stripped out and a copyright notice attached on behalf of the content owner (WMG). It says, "Matched third-party content." That's fair enough.
What fascinates me is how did they work out that the audio was, well, dodgy? Does anyone know how that happens? It can't be a manual process, can it? Someone playing all the videos and suddenly going, "Hey! I know that song!"?
EDIT: See 'Google seeks to turn a profit from YouTube copyright clashes' which seems to support Olly's answer, which is why I'm accepting that one.