I always prefer the window because you just never know what you might see when you look out. I fly SEA/PDX every week and never grow tired of the fabulous views (of course I realize that most commutes aren't this scenic).
The little commuter planes fly lower so we get a much closer look at the mountains, which never cease to amaze me. Every angle of light and level of clouds paints a totally different picture. Add in the beauty of the sound, the river and the cities and this is one of the most beautiful flights in the world. Of course, nothing compares with flying over the Glaciers going in and/or out of Anchorage one one of those rare crystal clear Alaska days.
There is also the sleep factor and I can sleep like a baby on planes.