At least with Jetblue I once read that they try to fill in the middle seats first so the earlier you check in the worse your ability to get a window or aisle...which is really contrary to anything I've heard...but it did happen to me, I once checked in for a JetBlue flight 3 hrs in advance and there were "no window or aisle seats available" (they did try to sell me a window seat for $40 which I refused), then another person who checked in just 20 mins before got a window on request...suddently they had become available!