Export keyframes as baked meshes? Looking for a script that runs through the animation frames and at each keyframe it exports just the mesh as a .fbx (no cameras, bones or helpers) at that specific frame, preferably with a filename that includes the frame number. 

If nothing like this exists, I'll attempt to write it myself soon, but I've never written a blender script before and it's been years since I used Python at all, so I may need some instruction (library reference or similar).

Using this output as an input for morph targets in another application.
You may get away with


Scene.frame_set
bpy.ops.export_scene.fbx


I.e. select your meshes and run

import bpy

PATH = "your_path.%03d.fbx"

for i in range(100):
    bpy.context.scene.frame_set(i)
    bpy.ops.export_scene.fbx(
        filepath=PATH % i,
        object_types={'MESH'},
        use_selection=True
        )


The source code of export_scene.fbx resides in scripts/addons/io_scene_fbx.