The reason files are displayed in hierarchies or trees, is that for the most part they actually are in hierarchies. Files are inside folders are inside other folders and so on.
If you want a program representing relationships between files, for instance, which executables rely on which dlls (in Windows) or other executable components or configuration files or scripts, I do not believe there is currently a tool the does this. It would require a programmer with an intimate knowledge of every program out there, or a master program capable of querying each and every file and finding each and every relationship.
On a related note, Windows Longhorn (what became Vista) was originally supposed to have a new file system that made folders and hierarchies less of an issue by effectively keeping a database of every file and then programs would just ask the database to get the file they want. This idea was dumped, unfortunately, prior to shipping. Windows 7 has folders that show in the My Computer view that aggregate all files of particular types from within your various user directories so that, by looking at one of these virtual folders you see all your documents, or all your pictures, regardless of where in your profile directory they actually exist. This is a similar but simpler application of what MS was attempting in Longhorn.