Moving our discussion back here from another thread.
Ok, just looked at the meshes and textures .bsa's, it looks like empty and filled soul gems both use the same meshes and textures, and all soul gems share a single glow map. You'd need to create duplicates of the nifs I think, remove the glow maps from them, then have the empty soul gem base objects point to the duplicate .nifs instead of the originals. What have you tried?
You are correct about the second set of nifs.
Changing the glowmaps from super neon bright to black has no visual effect in game. Some but not all of the glow is coming from the cubemaps. I have also discovered that the emissive and specular settings in nifscope have very little visual effect. Here is my current version, done almost all with the cubemaps:
http://i.imgur.com/wz1uM.png - here you can see that the glow isn't coming all the way out of the dimmer versions. Also both black gems are dull, because I haven't decided what to try and make glowing black gems look like.
http://i.imgur.com/pOg5t.jpg and neatly laid out for comparison. Those are black ones after the grands. There is some untouched clutter around for comparison.
http://i.imgur.com/e3Yi1.png - it is now becoming difficult to tell empty/full apart. I could give them separate base textures, but it would remove all compatibility with texture replacers. If I make the full gems much brighter than they are now, they appear as nearly solid white. You can also see Azura's star, which I have not touched at all yet except copying it's SLGM entry into my mod (it is basically a dirty reference for now).
Note the "JO" which is actually "Azura's star". Editing the SLGM entries makes their names into stuff like that. I hand-renamed the normal gems, but it means this mod will turn all gems English.
http://i.imgur.com/MTMRe.png - this is what they might look like on display. Not great. But if I dim them, they go back to being indistinguishable in a dungeon.