Personally, my method involves creating a folder, named of the title of the work. For instance, Challenges, for my fanfiction, or Short Stories, for my short story collection. Since I don’t often write poetry, they all get stuffed into a Poetry folder. All these are put in my Writing folder under the My Documents (and backed up to USB flash as well as Dropbox).
I also create a WIP folder which stands for Work in Progress. These hold all the current projects I need to focus on, from blog entries, to short stories, to fiction, to non-fiction pieces. I also add a ! in the front of the folder’s name, which put this at the top of the list when sorted alphabetically.
The Writer’s Relief post offers writers more methods on how to organize their writing with regard to publishing in that particular market.
I highly recommend you follow their site. It is incredibly useful.