OK
There isn't actually a huge difference between the before and after pics

At least it doesn't look like there is.
Here is what it looked like before I started

Along with how the cables were arranged behind the motherboard tray

The main mess was up in the top section. A lot of cables tucked into the 5.25" drive bays

After removing everything but the power supply, we can see how many power cables I have to deal with

I separated the cables I wouldn't need and tucked them behind the motherboard tray.

Then went crazy with the masking tape

It's a good thing that's going to be hidden behind a side panel
After completion it doesn't really look a whole lot cleaner.

The jumble of cables that was taking up space in the 5.25" bays has moved behind the motherboard tray.
The SATA power cable for the lower hard drive has been routed behind the mother board itself for a short run.
The wires in the upper half can still be tidied up a bit, need to break out the zip ties for that I think.
The SATA data cables are a problem, mainly because of where the headers are on the board. Don't know how I'd make those any better.
Temperatures do seem to be down a bit, as I gave the case a good dusting in the process

(and yes, I did remember to plug the 4 pin power cable back in after taking this photo)