Existing Animations

Wallace and Gromit - A Grand Day Out (1989)
http://www.youtube.com/watch?v=5jvOTsi3i64

A classic piece of clay animation. Although the characters don't have eyebrows, the emotions are still conveyed through the deformation of the top of their heads. When Wallace drips paint on Gromit's head, he is clearly annoyed, as his brow dips in the middle giving an expression of mild anger. In the same scene, Wallace is blissfully unaware and in his own world. His eyes are wide, his brow is relaxed and he has a small smile on his face. This shows he is content and enjoying his painting while not being the most aware of his surroundings.
When Gromit is drilling, he is surprised by the force the drill gives, causing his body and ears to vibrate. His surprise is shown by the sudden widening of his eyes and slight recoil.

Creature Comforts - Pets at the Vets
http://www.youtube.com/watch?v=5ecpYfWFmLA&feature=related

More clay animation from the same studio, Aardman. There are many examples of facial animation here. The sound is recorded and then the characters are animated to fit the voice. The hamster, for example, has a slow and droning voice, so the animators have given the hamster dreary eyes, he is mostly looking at the floor showing he isn't paying much attention and he is sitting still with his arms rested on the cage, only making a few small, lazy gestures.
Also, when the lioness is talking, we can tell the sound man off screen is scared simply because the boom-mic is shaking violently.