I\'m currently trying to export an animated blender model to three.js using the exporter of three.js (github.com/mrdoob/three.js/tree/dev/utils/exporters/blender/2.66/script
The problem was that the location/rotation/scale were not reset before exporting the model.
Before You export Your model, select the mesh and press CTRL+A and select location. Repeat for rotation and scale, then select the armature and do the same. Now it works.