Here's an example with a Flash project, but I'm sure a lot of projects are like this.
Suppose I create an image with Photoshop. I then export this image as a jpeg for integration in Flash. I compile the fla as an asset library, which is then used in my Flash Builder project to produce the final swf.
So it goes like :
psd => jpg -> fla => swc -> Flash Builder project => swf. => : produce -> : is used in
The psd, fla, and Flash Builder Project are source files : they are not the result of some process.
The jpg and swc are what I would call "intermediate" files. They are the product of one (or more) source file(s) that are used as input in another tool or process.
The swf is the final result.
So, would you keep those intermediate files under version control? How do you deal with them?