It’s been a long time…
Here is my latest creation, Make Faces Planar.
Select a bunch of faces in a mesh and make them co-planar in a single click!
Force Orthogonal (optional)
Force the plane to be orthogonal  Facing fully X, Y or Z, positive of negative (whichever fits better) .
Choose whether you want the faces to be projected across the whole selection or per face.
Each set of connected selected faces will be calculated together.
Make the planar effect falloff based on proportional edit settings, or approximation thereof Whichever Blender allows.
This was written for the latest Blender Trunk build, but should work in the official 2.7.2x release.
Comments and criticism welcome!
References [ + ]
|1.||↑||Facing fully X, Y or Z, positive of negative (whichever fits better)|
|2.||↑||Whichever Blender allows|