I have just barely started working with them. My thought is to have any laptop and computer in the house back up to a NAS so that EVERYONE's music is always fed to the ATV.
For my larger system's I think that you should always have some sort of Dock and Music server.
For my more modest systems $5 - $10 k I really haven't figured out the best solutions, we just did our first ATV system recently and so far it has proven to be great, but the family doesn't have a an ipod (yet) they just use iTunes as a way to manage their music.
Cory "you like our booties? Oh, you must mean the shoe covers."