I always try and book a window seat. Mostly because I am a bit claustrophobic, so looking outside helps me a lot!! I also look out the window all the time and take photos. I have some great photos over the Grand Canyon, the Tetons, Mt St Helens, Mt Rainier, well just about any mountain I've flown over really.
Oh, I have photos of the arch in Missouri from the air. They are pretty cool as well.
I just pop on the great big lens and go for it. No one seems to mind and it keeps my mind occupied.