Since so many of my add-ons use multiple folders within the Add-Ons folder, I sometimes lose track of which ones go together, or are current, when I download new versions of everything. To address this, I selected all the existing folders within Add-Ons and applied a color (label) to them. (This is in Mac OS X; I imagine there's something similar for Windows...) Then, after downloading new add-ons, I moved each of them into the official folder, which overwrote the old versions and removed the color/labels. This way, I can tell which folders have not yet been updated this time, and decide whether I want to update or trash them.
GB
(PS: the add-on folders that start with "Blizzard" are official WoW items, and only get changed by official patches, so leave them alone.)