Here at FaceFX, we frequently get asked if we support Blender. With FaceFX 2013, we are taking a big step towards that goal with our new FBX pipeline. Just create your character in Blender, add an animation that specifies the poses you want to drive in FaceFX, then export an FBX file and drag it onto FaceFX 2013.
The pipeline sounds great in theory, but I'd really like to hear about problems people have. So please take a look at the FaceFX 2013 Beta, and let us know at support (at) oc3ent (dot) com if you have any difficulties.
You can download the Beta from here
If you are taking animations from FaceFX directly into Unity or UE3, then you should have everything you need with FaceFX 2013, but to get animations back into Blender, we still need to figure out a good import pipeline.