Here's my system:
Folders -Done, Projects, Reference, Review, Tickler, Calendar support. Also a few AOF support folders.
I use the same folder setup for Outlook and My Documents.
I also use Onenote with a similar setup to summarise information and keep links, and working notes.
Project folders have subfolders - #Project, +Done, +Information, then one subfolder per sub project.
the # and + are used to keep those folders at the top of the list. A sub project could be a meeting, a document review, basically smaller tasks within the same project. When I've completed a subproject it gets moved to the Done folder. The project folder holds discussion notes and emails/documents related to the planning and management of the project. I use information folder to hold project support information.
Reference folder is for general reference, and may duplicate the project information, but usually doesn't. If I have an active project for stuff then I would preferentially file it there, and when a subproject or project is done but I want to keep the stuff, I would move it to reference then at the end of the project, or just move the whole project to a Done folder.
Document Version control - I've struggled with these issues too. I've now decided that each version is a subproject, and gets its own subfolder within the project folder. Each version might have several steps (drafting, reviewing, comments), emails for it would get stored in that subproject folder. When that version is finished, the folder gets moved to Done, and I make a new folder for the next version. When the document is finalised, the final version gets stored in Information, and on the company filing system.
What I like about using a folder for Done items, is that your filing system is not cluttered up by completed stuff, and basically consists of all your active projects and open loops. You get a real clarity about what needs to get done, whilst still keeping the completed stuff as reference within the project.