How do you organize and clean up custom files?

The wiki has some general info which can be really useful. Other than that, it really depends on what you want, what CC you have and what works best for you. For TS3, I play it almost vanilla, so it just has some NRaas stuff and some things from MTS that are each in their own folder. For TS2, I have a lot more Those are all foldered by creator and then by set as the creator uploaded them. I usually have a txt-file inside the folder with a link and TOU. I've heard people put swatches inside those folders too, but I'm not sure if this affects loading times. I clean them up in two different ways. I tend to go on big downloading sprees, which I then put in one big folder, not yet in my game. I slowly move them from that folder to my actual game folder, so that it's a second check whether I really like the CC or not. When I don't use a particular item in-game or think it looks very ugly, I make a note of it so I can delete it immediately when I'm finished playing.