There's a lot of learning material in the DirectX world that uses .fx files to manage shaders, and .fx seems to be well integrated with 3D packages such as Maya and 3D Studio Max
What do larger OpenGL projects use? Do they all have a bespoke format or are there any common standards in use that might have some tools to go with them?
Can you use .fx files with Cg as the languages are so close syntactically? I hear that Cg has poor performance on the ATI Linux drivers but at least it my help me get going on my own Nvidia system.