Unity iPhone: difference between shader and iPhone-shader?

The most important difference is that CG/GLSL is not supported in Unity iPhone. (The original GPU is fixed function only.) You can find more information here:

file:///Applications/Unity%20iPhone/Unity%20iPhone.app/Contents/Documentation/Documentation/Manual/iphone-unsupported.html

Knowing that, nearly everything found in the ShaderLab Reference will work on the iPhone. I agree with you that the differences need to be documented, however. Here are a couple things, that I know of, that aren't listed as not working, but still don't work:

• Cubemaps
• SeparateSpecular command
• Three-argument texture combiner functions (except Lerp)
• GrabPass

Every shader included with Unity will work on the iPhone, but that's only because of Fallbacks. Generally, if you don't want to write your own shaders, it's a good idea to use the ones in the iPhone standard assets, because they are designed to run a little faster than the non-iPhone stuff.

Edit: Re-reading your question, I'm thinking perhaps you mean that the iPhone shaders should have documentation such as is found in the Built-in Shader Guide. Although I agree with that, the shaders that can run on the iPhone are much less complex than most of the other shaders, so it's to every Unity iPhone developer's benefit to learn the simple ShaderLab language, and write their own very fast shaders. As it is, a couple of us have begun adding this kind of extremely fast, simple shader, to the wiki. Glancing over them would probably be a good way to help yourself learn, if you're interested:

http://www.unifycommunity.com/wiki/index.php?title=Shader_Archive#iPhone