That waving standard is very impressive. I didn't think things like that were possible with shaders.
Is there anything else like this that's possible that we don't know about?
I didn't know that we add access to shaders, either! Yes, there is probably a lot that can be done, but me must think stuff, it is not like there a list of things to do. It is more like general, but constrained, programming. For example, it turns out that, if native didn't have reflective water, we could have programmed it ourselves for our Mods. I mean to say that reflective water is something Aramgan did (or his staff did), but it is not hard wired in M&B. I am quite experenced as shader writer, so propose stuff, and it might be doable. For example, red glowing lava "water" in the background, anybody? I made it as a test, but found that it looked nice.
Also, when you say there's no way to have specular and transparency on the same object, I suppose it's not possible to have more than one alpha channel?
A specular/transparency shader would be really handy for quite a lot of people. Well, it would be handy for me, at least. 
Of course, you can have a fully specular object and alpha-based transparency. But the alpha channel of the texture is mapped either on transparency or on specularity.
Hum, no, you can't have a 5 channeled texture, but here are several ways out of this problem, that might be or not be useful:
1) have per-vertex alpha color dictate transparency, but texture alpha channel dictate specular coefficient (or viceversa) -- this requires another ad-hoc shader.
2) Use one of r,b,g channel for transparency, alpha for specular. The missing color channel can be made up (for example, assume R=G or R=G/2 or whatever).
-- this requires another ad-hoc shader.
3) Use alpha for transparency, and a second texture for translucency (edit: this is what people has been doing). But, I find it boring to edit, handle, load, and consume memory for two textures. Also, additional texture accesses are not free, performance-wise.
When possible, I like the 1 because it is pretty general and cheap on resources.
For these who missed it, vertices can be singularly colored, using BRF edit, or even hacking BRF files with an HEX editor (or in other ways as well).
Normally, RGB color of the vertex (interpolated across the polygon) is mixed (multiplied) with the color coming from the texture.
But the shader can be written to act differently, for example in 1) above.
