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.