DaVinci Resolve Lite – free:
- http://www.sonycreativesoftware.com/forums/ShowMessage.asp?MessageID=758711
- http://www.blackmagic-design.com/press/pressdetails/?releaseID=11851
- http://www.blackmagic-design.com/products/davinciresolve
- http://www.blackmagic-design.com/support/detail/?sid=3948&pid=11735&os=mac&leg=0
The full version has 3D tracking “Power Windows”, so you don’t have to manually generate and track masks. It is said by some to be runnable on linux.