Conceptually such a tool would be very handy as it is typically a very awkward task to find stray files and safely remove them.
I'm not sure if this is the case... but from the wording of this question it looks like this might be a self-promotion question which isn't an endorsed activity. If you wanted to follow up to the generic question "what tools are out there to do x,y, & z" with your own answer that would be fine.
For the record, I use 2 tools called CheckWeb and Xenu that will follow all links and report back what was found.
This finds me any 404's, and I then compare the list of referenced files against my directory listing to see what files were not used. (Its rough, but works)