If it wasn't for Microsoft Excel . . . well, I'd probably find another spreadsheet program to organize my writing. Although, now that I think about it, I've worked with other spreadsheet programs and Excel seems to "excel" above the rest. If you don't believe me, a recent post by marketing guru Seth Godin tells all.
Whatever works for you to organize your writing, use it.
My method of madness are Microsoft Excel spreadsheets. I have a master spreadsheet, where I have a "worksheet" for each novel, a worksheet for a summary of all of my novels, and even ones for my short stories.
Submitting to agents or publications? Keep track of who you send your queries to, because if you don't, you're bound to send it to the same one twice--been there, done that, got the T-shirt.
If you're going to be a successful writer, you need to be organized enough to know what stage your projects are and where you're at. Even for editing novels and new novels, I have a separate spreadsheet showing the current chapter I'm working on, the number of pages, and the number of words--because, somehow, agents and editors want to know how many pages you're book is, and if you're keeping track of it, you can have that number right at your fingertips (pun intended).
I can't stress enough the need to be organized. Act like a professional, and others will take you seriously.