Go to the Sound Preferences window (System -> Preferences -> Sound)
Click the tab all the way to the right that says Applications
This tab lists programs using the ALSA plugin and allows you to mute individual programs
edited for clarity, original below:
Try right clicking on the speaker icon that is in the top right corner by default and go to sound preferences. Click the tab all the way to the right that says Applications and it will give a list of all programs using the ALSA plugin and allows you to have separate volume control over each of them as well as muting individual programs. Hope thats what you are looking for.