It depends a lot on the used engine (supported APIs, input parameters etc). If you have an engine which supports DirectX, then take a look at the shader designer of VS 2013.

A while ago I wrote this post. As part of my 3d engine I wrote this shader generation tool that takes a node graph and generates its associated shader code. It is not (yet) visual as VS12's shader designer, but I'd argue it is easier to integrate into your own engine. When a shader is generated through the tool, the system writes some metadata so that when the shader is loaded back into the engine, it know where to fetch the associated parameters.

For example if you define a constant buffer containing a world matrix, then the engine will know that the world matrix refers (for example) to an entity's world matrix and will know how to fetch the relevant matrix accordingly. In this way you don't need to write any ad-hoc shader initialization code on purpose.

You can check it out in my GitHub repository, look for the OdysseyTools.sln file.