Google My Tracks, make sure you have pre-cached your maps though as you won't get a signal to download the maps above around 5,000ft. This will record your route for future playback too.
Just be sure to turn all the sensitivity/accuracy settings as low as they'll go - it's tough keeping a signal on a plane and you may end up with gaps otherwise.
The results can be amazing :-)
Map created by GPS Visualizer
Map created by GPS Visualizer