If you like the convenience of Apple's pre-defined function keys but sometimes need them to be regular function keys for a particular app or two, Palua can help you out. It provides a means of quickly toggle which mode you're in, and can even automatically switch based on which app you're currently using.
After installing Palua, you just press Command+Option+Tab (a shortcut that you can change) to toggle between using your function keys (F1, F2, etc) as standard keys and using them with the special features printed on each. This is handy on its own, but what makes Palua really cool is its ability to remember your preferences. If you enable Smart Mode in its preferences, whenever you toggle between regular and special key mode Palua will remember your choice. From then on, when that app gains focus Palua will automatically set the toggle for you so your functions keys will work the way you want on an app-by-app basis. That's all it does, but if you've ever found an occasion to need this you know how useful it can be.
Palua ($1.19) [Mac App Store]