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I would like to know if there is any application that can enable you use use Fn keys differently based on the current application.

For example in terminal or you favourite IDE you want to use them as standard function keys but for other applications you want to keep the default Apple keys.

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FunctionFlip might be what you're looking for.

FunctionFlip's purpose is simply to disable the special features — rewind, play, mute, etc. — on the function keys. For example, if you "flip" F7, F8, and F9, those keys — only those keys — will revert back to normal F keys. Press the fn key with the special key to get the special function back. That is, the "special" and "normal" functions are flipped.

To assign a custom shortcuts to your reclaimed keys, use a program like Quicksilver or Keyboard Maestro.

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I've edited your post with more information, @ron, but just pasting links is not how things work here. Please the the faq for more. – Loïc Wolff Oct 25 '11 at 15:51
@LoïcWolff No problem. – ron Oct 25 '11 at 18:20

Palua will do exactlly what you need.

Introducing Palua, the easy way to quickly switch the mode of your Function Keys on any Mac keyboard!

You need to run a game, or start a graphic application, or work on a project that need F1-F12 as function keys, just hit option+command+TAB and the switch will happen.

Smart Mode: Key mode changes with the application that has the focus.

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The link to Palua doesn't work, go here – fredw Jul 11 '15 at 6:49
Unfortunately Palua doesn't work with el capitan. I ended up setting the default to function keys (with keyboard pref pane) as I generally use those and using Keyboard Maestro to remap some of them back to the special apple keys. – jonaustin Nov 26 '15 at 18:19
As of today Palua has disappeared from the App Store and internet in general. – krs013 Mar 10 at 4:46
I am not certain, but I think Palua used to work on El Capitan. I tried running it from bash, /Applications/, but got this error. "2016-03-19 23:07:40.302 Palua[21714:183915] Palua must exit, the Mac Apple Store Receipt is invalid." – sigjuice Mar 20 at 6:11
@ksr013 I was very disappointed not being able to find Palua any more. I started to love this small app. Any idea where it could've gone? – preeze Jun 3 at 10:09

I don't know what keys you need, but for me the easiest solution was to use all of them as standard function keys amnd using bowtie with global shortcuts to keep F7-F12 as media keys, while having F1-F6 as standard function keys.

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