I use an ancient program called Writenow 3 to keep track of SDFs. (It opens fast but it's more versatile than Textedit.) In my experience, keeping track of SDFs is vital if I use them more than three times (which I do...)
I've used Appleworks (the spreadsheet is similar to excel) to make a table of the Blades of Exile items. I use that when I need a lot of custom items and/or have to put a lot of items into a different order.
I scribble some notes on papers, too. Especially the general ideas in the beginning. And I map them. If the scenario making project is big, I draw a map of the more detailed plotline(s).
I also keep track of where spells and recipes are sold and other minor things, mostly ideas about what could be cool...
Some monster graphic sketches I've drawn on paper first. I use another ancient program, Superpaint 3, to make my custom graphics.