I wrote a little fix for Beyond Good & Evil, which should apply letter and pillar boxing to display the games 16:9.4 image without stretching on any resolution. It might break game overlays though.
Download: http://www.goo.gl/2Cltb
Just drop the files in the zip in the same Directory as the BGE exe. Also if you've changed the NoBands value in the registry, you should change it back to 0.

If you get an Error message like "DirectX 9 was not installed properly" or "This application has failed to start because D3DX9_43DLL was not found ", you first need to run DXSetup in the Redist subfolder.