Apple - Can I use my F1, F2, etc. keys as standard function keys only for specific apps?
Try Palua, I think this is exactly what you're looking for. Costs $0.99 / £0.69 in the Mac App Store.
In MacStories: Control OS X Function Keys with Palua
Fluor is exactly what you're looking for. You can chose either default (the settings you can adjust in your system preferences), apple-keys or function keys.
I hope that was helpful!
I've seen this application before when I was just browsing, never used it though. It's called FunctionFlip.
FunctionFlip individually controls your MacBook or MacBook Pro's function keys, turning special keys back to regular F-keys, or vice-versa. FunctionFlip is a preference pane; you'll find it in the "Other" category in System Preferences.