Everyone develops his own methods for organizing plugins.  I keep them in two lists: I maintain a section in my downloads directory /home/<me>/downloads/SC4RelatedDownloads which is broken down further by author or authoring group.  I keep all original downloads whether they be programs or plugins. My /home/<me>/SimCity 4/Plugins directory reflects this organization as much as possible.  Some installations (NAM for example) override my basic structure but I live with that. I assume you meant file structure and not file system.  If you are running Windows your file system is NTFS (New Technology File System) which has been around and retuned from time to time since before XP.  Mine is a virtual system, ext4, sitting on top of gvfs (GNU virtual file system) which accommodates many different layouts including NTFS.  Please note that all this has to do with the fact that I abandoned Windows in 2007 and have never regretted it.  My structure was developed while I was on Windows and all I really did was import it.  For /home/<me> think C:\<your account>\.  I don't have a catch all Documents folder.  My Documents folder contains my personal stuff and has no relation to the operating system.  It is /home/<me>/Documents and contains only stuff I put there, and the system installers put nothing in it.  When you initialize a new system, however, this folder is created automatically as I recall.  I haven't done an O/S reinstall in over a year.  I guess I was spoiled by Multics and UNIX, since I used both of them when Bill Gates was still in high-school.