I need a tool that can generate a tree for a C application. like walking through it to build which methods is called
I think "best" is really subjective, but eclipse and eclipse CDT have loads of plugins.
This thread is probably relevant.
If you want a thing of absolute beauty shell out the money for Klockwork.
EDIT:Thought I would add this since the user complained about requiring an IDE. I would really rather do it from an IDE myself, but there are other options.