I want to have a Cube in scene A, and linked in scene B, but with different material.
The solution for this problem was found on BlenderArtists.
click the material tab and you will see a little drop down that says "dat" or "Data". Click that and change it to "Object". Now you can assign the material to the object instead of the mesh or "Data Block".
But what if I have 5000 Cubes in scene A, and I want 4999 of them to be in scene B with different material X, and 1, with material Y.
If I try to "link material" in scene B, with new material, it won't copy "Object" selection. I would have to go over 4999 cubes and change them to "object" in material tab.
I can't join them, and then separate - all objects are in a mess after that (and blender crashes anyway).
Material override for whole scene won't work for me.
Is there any option to override materials in groups? That would solve the problem in some way.