I know someone mentioned the people yelling SUTA during Phantom's shows. I've noticed that you can hear it in each of the last few years, at least 2003-2007.
My favorite though is in PR '07. Right at the end of the Flower Duet, the two players cut off, and there's a pause before the audience begins clapping, and you can clearly hear one guy go "Yep!". Nothing major, but makes me laugh every time. It's at about 4:45 on the recording, and you might have to turn your speakers up a bit.