You've been there...
Maybe you're listening to your favourite song on Rdio, or maybe checking your Soundcloud stream. You reach for the play/pause key on your keyboard and BAM, motherfucking iTunes comes up. Don't you hate that? I do.
Luckily, there's a way to fix it. Open your terminal and type:
launchctl unload -w /System/Library/LaunchAgents/com.apple.rcd.plist
Voilà, iTunes no longer responds to the media keys. The only downside is that now iTunes doesn't respond to the media keys at all. I couldn't care less, but if you're a crazy person who actually likes iTunes (poor you!), you can reattach the keys at any time with:
launchctl load -w /System/Library/LaunchAgents/com.apple.rcd.plist
One could conceivably run the detach script at login and write a small AppleScript launcher to reattach the keys and then launch iTunes. I'll leave this as an exercise to the reader.