Yes definitely. +1 for a customized graph view. I can see so much potential in this.
Example scenario:
For example as a student, I classify my study material in three categories: definitions, concepts and synthesis. And they both have reference with each other. I can link them all I want, which makes it very powerful for jumping from reference to reference. And I can see all these links in the graph view. Now what would also help is to distinguish between the different type of file. Say definition in green square nodes, concept in blue circles and synthesis in red rectangular nodes.