Puedes intentar usar un private.xml como este con KeyRemap4MacBook:
<?xml version="1.0"?>
<root>
<item>
<name>test</name>
<identifier>test</identifier>
<autogen>__KeyToKey__ KeyCode::F1, VK_CONTROL, KeyCode::BRIGHTNESS_DOWN</autogen>
<autogen>__KeyToKey__ KeyCode::F2, VK_CONTROL, KeyCode::BRIGHTNESS_UP</autogen>
<autogen>__KeyToKey__ KeyCode::F3, VK_CONTROL, KeyCode::EXPOSE_ALL</autogen>
<autogen>__KeyToKey__ KeyCode::F4, VK_CONTROL, KeyCode::LAUNCHPAD</autogen>
<autogen>__ConsumerToKey__ KeyCode::F5, VK_CONTROL, ConsumerKeyCode::KEYBOARDLIGHT_LOW</autogen>
<autogen>__ConsumerToKey__ KeyCode::F6, VK_CONTROL, ConsumerKeyCode::KEYBOARDLIGHT_HIGH</autogen>
<autogen>__ConsumerToKey__ KeyCode::F7, VK_CONTROL, ConsumerKeyCode::MUSIC_PREV</autogen>
<autogen>__ConsumerToKey__ KeyCode::F8, VK_CONTROL, ConsumerKeyCode::MUSIC_PLAY</autogen>
<autogen>__ConsumerToKey__ KeyCode::F9, VK_CONTROL, ConsumerKeyCode::MUSIC_NEXT</autogen>
<autogen>__ConsumerToKey__ KeyCode::F10, VK_CONTROL, ConsumerKeyCode::VOLUME_MUTE</autogen>
<autogen>__ConsumerToKey__ KeyCode::F11, VK_CONTROL, ConsumerKeyCode::VOLUME_DOWN, ModifierFlag::OPTION_L | ModifierFlag::SHIFT_L</autogen>
<autogen>__ConsumerToKey__ KeyCode::F12, VK_CONTROL, ConsumerKeyCode::VOLUME_UP, ModifierFlag::OPTION_L | ModifierFlag::SHIFT_L</autogen>
</item>
</root>
No sé si funciona con todos los teclados, pero sí funciona con mi Kinesis Advantage.
Consulte enlace para obtener más información sobre el uso de KeyRemap4MacBook.