TUAW has been able to confirm that FaceTime works just fine on Wi-Fi equipped airplanes.
The reader who told them about it managed to video it (see below). You'll see the call actually goes pretty smoothly except for some little, forgivable video hiccups. This is really nice to know. Also, it comes as a bit of a surprise, as most in-flight Wi-Fi offerings tend to block services like VoIP. Simple oversight? Probably. Yet, we're hoping it's one that's going to last:
Impressive stuff, right?