The music video for 'Travel is Dangerous' by Mogwai was created by the artist Monkmus. It depicts alien creatures fleeing their crumbling planet through textured illustrations. Monkmus also created the video for 'I Will Follow You Into The Dark' by Death Cab For Cutie.
While this isn't stop motion animation, I LOVE the simplicity of telling a story through still drawings within a moving video. It may be worth a try.