Maltaannon (as Polygon Studio) is previewing a new After Effects filter, MotionGrabber (Windows-only for now), that he's been working on with Avidion Media:
"It is meant to help you with uncommon motion tracking tasks that are hard or even impossible to handle with After Effects build in pixel tracker. I welcome you to download this plugin and give it a try. MotionGrabber 0.0.1 is a early prerelease that was tested only with After Effects CS3..."
Go to Maltaannon for more info and the download.