There are subtle, precise controls for getting your Facebook privacy back the way you like inside the social network's settings. If you want the nuclear option — no Facebook app messages or pings forever — tech blog Digital Inspiration shows you the switch.
As the tech blog explains it, there's an option inside your Privacy Settings, in the Applications and Websites section (which you might easily miss) that cuts off the "Tim sent you a Golden Egg"-type notices for good. It's explained in the screen demonstration embedded above. As the post notes, this option will also disable any synchronisation you've got going from Twitter to Facebook, your blog to Facebook, Facebook to Twitter or the like. Then again, if Facebook is where you just want to connect with people, you'll probably get by just fine without any app exposure.
How to Block all Facebook Applications from your Facebook Profile Forever! [Digital Inspiration]