Okay, so I may be giving in to my resistance to pop culture and pick me up one of those fancy new iPod Shuffles soon.
There is an operation limit of 10,000 feet. But what about inside an airplane?
A Google search came up with reports of regular iPods not working at the top of mountain hikes, etc, because the hard drive platters can't operate at altitudes above ~10,000 feet due to cushions of air created by the spinning of the platters with such thin air.
BUT, the iPod Shuffle uses flash memory instead of a hard drive, and commercial passenger airplane cabins are pressurized, and I know people use their laptops on airplanes all the time (e.g. hard drives). And, I have never heard of a 12 year old freaking out because her iPod didn't work on an airplane in the first place.
So, I conclude that cruising at 36,000 feet in a commercial airliner isn't a concern in regards to using an iPod Shuffle above its 10,000 feet limit.