When using document libraries in SharePoint try to avoid the temptation of creating nested folders. There are several reasons you do not want ot create folders more than one level deep if you need to create them at all.
Instead of creating folders in Document Libraries create a seperate document library, this allows users to consume the content most important to them and you have more control over security and other features such as custom views.
Q: When should you use folders?
A: Archiving documents - maybe you archive all documents for a year in the 2004 folder or if you have a lot of documents being added like meeting minutes maybe you add a folder for the month and archive all the meeting minute documents for a given month.
Note: A single level of folder structure is generally ok when you really do not desire to create a seperate document library for one reason or another however avoid going 2 and 3 levels deep (keep in mind these are just guidelines).
Q: How do I keep related document libraries together on a single page?
A: Create a web part page and add all of the document libraries to that web part page. An example would be multiple document libraries for a given project, you would create a web part page called 'My Project Documents'. Then you could take your Design, Models, Requirements, User documentation document libraries and store on the new web part page you just created.
Hope this helps...
Edward J. Ferorn