Scarybob and kirjtc2 have it exactly right.
Depending on where you got the signal from, it has an identifier embedded in it.
This identifier is undetectable by humans, but it can be picked up by computers (even after you re-encode, sometimes)
The signal is the 'new century' way of recording TV viewing habits (e.g. Nielson viewers) - instead of having to press buttons and all that to determine what you're watching, the new tech uses a recording device (like a mic) to listen to what you're actually watching, for how long, do you change the channel at commercials, PVR it and watch later, etc. (or at least tv viewing polls is one use for it that I know of.. it may serve other uses too)
Using this signal, the networks (or possibly even individual channels) can input the ID and have youtube perform a scan. If your clip is long enough to have the readable code, it might get picked up.
However, if the clip is short enough or its a remix, etc. You can probably make a dispute and someone will manually check your video to see if its within creative rights or not and you might get it put back up.
Generally, the US stations all use this technology. As far as I know, most Canadian channels do not (yet), or at least don't have youtube scan for it.