I have tried baking a lightmap on two computers while using the self illumination shader, and it seems that the 3.5 version doesnt bake the Emissions (lightmapping.) like on the video(Unity 3d Beast Lightmapping Tutorial - YouTube).
Has this method changed or is it just me?
I ran into the same issue as you, and agree that the information on this subject is VERY confusing.
My current understanding is that while Unity Free does support emissive shaders, they will ONLY light the object they’re applied to. Lighting of the rest of the scene requires GI lightmapping, which is only available in Unity Pro.
I’ve confirmed this by loading my test project (which produced a completely blank lightmap in Unity Free) into the trial of Unity Pro, where it works a treat.