On the Short Mystery Fiction Society list, a writer mentioned my "formidable production" and asked how I organize it.
If you write fast enough, you don't have to be organized. I have several hundred short stories in various stages of completion--ranging from one-sentence story descriptions to multi-thousand-word near-final drafts. Whenever I see a call for submissions that piques my interest, I take a quick stroll through the WIPs to see if I have anything that fits. If I do, then I finish and submit the story. If I don't, then I try to brainstorm something appropriate.
But most of my work goes to publications where I've been published before. Mastering a publication's requirements means I don't have to wait for calls for submission to cross my desk before writing and submitting stories.
But how do I organize the several hundred partial manuscripts? File folders on my computer labeled by genre or by magazine or by series character. If I have an idea for a Morris Ronald Boyette story, the partial goes into a folder named "Boyette"; in I have an idea for a confession, the partial goes into the folder labeled "confessions"; if I have an idea for a Woman's World story, the partial goes into the "Woman's World" folder.
One tip if you write for contests and anthologies: Get a three-ring binder. Print out the submission requirements or contest rules. Put them in the binder in due date order. When you sit down to write, open the binder to the first page. Write a story for that anthology or contest. If you finish in time, submit the story and tear the page out. If you miss the deadline, tear the page out. Either way, the next time you sit down to write, open up the binder to the first page and write a story for that anthology or contest. Repeat.
4/29/9 addition: I keep hard copies of all my finished manuscripts, so the torn-out page goes in the file folder with the hardcopy so that I know how to follow-up later if I need to.