After Windows shuts down, the case fans and lights stay on. It's just an inconvenience, but I'd like to iron it out.
It didn't always do this, and it solved itself for a time. I don't remember when it started, but the first time I tried fixing it coincided with my dying PNY 9800 GT GPU which was causing my system to lock up for hours on end, forcing me to hold the power button down to shut it off.
Soon after I pulled the graphics card, I vaguely remember finding a forum post about the Power Options being a cause, something like the timing of displays powering off, and fiddling with the options. Not long after, I believe it started shutting down fine, but not immediately after I changed the options.
I reset the CMOS a week or so ago, and then my computer didn't get shut down overnight for a few days. The next time I went to shut it down, the fans and lights stayed on and that's where I'm at right now.
I'd like to add that I changed powersupplies after the problem started, but it persisted.