This problem does only occur with MacOS X v10.1 or later: If you insert a new Audio-CD while the game is already running, iTunes will be started automatically in the background. iTunes will get the active application but will not be visible if you are in fullscreen mode. To gain back control over Quake you should hit the mouse button once or hit "Command" and "Tab" until controls are back.
Open "System Preferences".
Switch to the "CDs & DVDs" System Preferences panel.
Set "When you insert a music CD" to "ignore".