How can I set up a Sonos system (and which system should I use?) if I have an AV receiver driving a home theater setup in the living room, an AppleTV (w/ Airplay) and various rooms in the house?

If you have an Apple TV already, I'd recommend getting Airport Express (http://www.apple.com/airportexpress/) base stations instead. That gives you a choice of analog or optical out in whatever room you place it in. They join your existing wireless network or can be hard wired, they act as clients to the wifi network or can also act as repeaters/extenders if you like. They show up on your Apple TV as an output device (I believe) and also on iPhones/iPod touchs/Macs in any app using the standard SDK volume controls, eg: When you compare the cost of Airtunes vs. Sonos it's ridiculously more cost effective.

Well in the home theater, the Sonos Connect will attach to your receiver.  In the additional rooms if you have no speakers you need either the play 3, the play 5 , or my preferred method the Sonos Connect amp connected to a pair of speakers, in wall floor standing, doesn't matter.  The Apple TV is pulling your iTunes data, movie and audio.  The Sonos will stream your iTunes music playlist and all.  So realistically, if you only using the Apple TV for music it would be redundant.  However the Apple TV is a great option for video.  We have several very high end setups where we used the Connect, into a DAC then into a McIntosh amplifier to great floor standing speakers with a crazy sub.  The system is very flexible