In FileMaker Pro advanced, you also can generate Database Design Reports. This may or may not serve your purposes. Files such as PDF's can be stored in container fields and opened for view or editing. FileMaker can generate PDF's with the save as PDF option if you need it.
And you can add comments to Relationships, scripts, Calculations and field definitions if you need the resulting "internal" documentation.
The Free Calendar from SeedCode has a good example of inbuilt documentation.
SeedCode's Hierarchy Template can be useful in creating structured documentation
Other Free Templates for examination
Starting Point 2
Data For Life
A Useful New Filemaker User White Paper
The Computer Guy, Seattle