I thought the same thing as I was reading John Siracusa's review of Mountain Lion. My stomach sunk when I saw the default 'gatekeeper' options.
[ ] Mac App Store
[x] Mac App store and identified developers
[ ] Anywhere
Seems likely at some point down the road the third option will no longer exist. My next project is getting Linux to run on an old MBP. I still love their hardware, but OSX is getting fuckin' uppity. I realize that this is just an attribute on a binary that you can set and unset, but still, the direction this is going seems clear to me. The further iOSification of OSX is driving me back to Linux on the desktop.
What's wrong with Apple trying to control which binaries it will and won't let you run on its OS? Doesn't Apple always have your best interests at heart?