Imagine, for example, that you need to stop the Zygote service and start it again later, because you're toying with Android internals and Zygote is getting in the way.
Or maybe you want to test out a new bootanimation binary, and for some reason running /system/bin/bootanimation directly is not what you want.
This is what you do instead:
setprop ctl.stop zygote
setprop ctl.start bootanim
Simple, right? Then how come it's ungooglable?
You can do all this from Java too, just use System.setProperty(). See this article for more detailed info about properties.