I also use the spreadsheet method for tracking. I have columns for file name, description and keywords, and a couple of columns for each agency the file is uploaded to. Coding is as simple as Pending, Active, Rejected and Black (for those that have yet to have anything done to them). I also break-up my images into broad categories to give me some summary info on the type of images that are working.
I've recently modified my sheets to give me some overall totals so I can see where there are more photos still to add (as cascoly when agencies come and go).
I don't file my images in stock specific folders but everything is labelled by date and that date info is stored in my spreadsheets so I can find them.
Currently I'm not tracking my sales figures in any effective way because I'm not selling that much

Perhaps when the sales come rolling in it will be more worthwhile.