Exporting an animated armature with a mesh for Unity using Blender 2.5 can be a bit of a hassle. With the armature parented to the mesh, I could either export the mesh or the armature with the animations, but never both.
Having the armature separate from the mesh seemed to have worked – I have now everything set up in Unity, both mesh and armature with animation.
Though the animation looks slighty wobbly …
This might work for simple animations; more complicated set-ups might still fail to export, since Blender 2.5 and Unity3D 3.0 both have not exactly extensively tested.