Take a look at some of the third party design tools offered. Some take the xml output from a FileMaker Advanced generated Database Design Report and do some very interesting analysis of your database.
Using just the database design report produced by Advanced, I sometimes go to the relationship graph, modify a table occurrence name by inserting something distinctive, such as "xxx" at the begining of the occurrence name and then generate the DDR and do a text search of the report for that text. I can often jump very quickly from reference to reference in the report to determine where or if that table occurrence is referenced. That can usually tell me whether or not I can remove that table occurrence from my graph pretty easily and sometimes will also highlight for me areas where I can update the design of my script/calculation/whatever so that the occurrence becomes redundant.
I happen to be using that method to gradually transistion two huge "spiderwebbed" systems into ones organized more or less into an Anchor Buoy format.