The following article from Macworld describes a new patent from Apple to detect jail-broken iphone/ipad. It also gives an interesting security twist on that patent, where it is in theory possible to take hidden photos and voice recording of a potential thief, analyse the accelerometer data to define if the thief is walking, driving or even flying, get GPS location, etc.
http://www.macworld.com/article/153612/2010/08/apple_mobiledevice_patent.html

I also came across that app for the iphone, which does not go quite as far but highlight the fact people have already thought about this:
SpyTools for iphone