Aisle:
Pro: Easy access to bathrooms, galley; quick egress at arrival
Con: Have to get up when other people want to go to bathroom; get hit by FAs, carts and other pax, limited window view

Window:
Pro: Window; ability to lean up against wall; away from noise/traffic
Con: Have to get ask everyone else in row to get up when you want to get up; can be trapped in upon arrival; claustrophobic when you're sitting next to a large or disgusting pax

On shorter flights I prefer the window because it's quieter and I don't have to worry about being distrubed by having to get up and let the other person out.

On long flights I prefer the aisle because I want to be able to get up and walk around or use the bathroom (I drink a lot of water on long-hauls).