We've traveled several times lately, both before and after September 11th, with a DeLorme Earthmate GPS receiver that plugs into my laptop.
I've had great success with tracking when sitting at a window seat (receiver slipped between the inner window and the pull-down screen works great. No success in the aisle seat.
On UA have only been questioned once, by the 1st Officer, and he only wanted to verify that the device was certified -- no problem.
On AA, was stopped and pointed out that GPS is on the "prohibited" list, as mentioned above in this thread, and is specifically listed in the in-flight magazine.
OT: Took the setup on a Miami - Western Caribbean cruise, and it was great. Using the Street Atlas USA software from DeLorme it tracked us across the US to MIA, then tracked the cruise down the coast of FL and showed the coastline of Cuba (not identified as such), the islands of Cozumel, Grand Cayman and Jamaica, also without identification, but all with geographic orientation, and tracked our "altitude" of 3x,000' on the flights and 80' in our cabin on the boat.