I just went through about four chapters of my WIP and added in a thread with my villain, making him increasingly, well, villainous. I've always thought that this was easier to do than the other way of just writing it in the first place. I guess it's part of the revision process, but it occurred to me about 3/4 of the way through that I needed to do this. Unfortunately, this meant resending a chapter or so to my crit buddy so she could read through the additional thread.
So in order to keep up with what POV I was using, and where this thread shows up, I started a spreadsheet of sorts to keep up with scenes and what happens. Eventually, I'll use this for my chapter-by-chapter synopsis. But it saves SO much time (duh!). I can just click on my chapter synopsis and know which chapter to bring up in my word processor to access what scene. (This may sound very simple to those of you longer in the biz and with more common sense, but I've always written my stories all out in one document, so I could just scroll through at will and see what I wanted to see. But being a part of crit groups, etc., working in chapter units is essential...so this had been a s t r e t c h for me. But a good one. :)