...I use a metal bore bit (not sure what it is actually called) that is shaped like a cone.
You're gonna love this. It's called a "tapered reamer."
The "secret" (if you want to call it that) to really amazing cable management is to get as many cables and wires as possible "behind and/or under" the main board. TD's photo above is a good example of this: the power cable bundle and the SATA cables attach to the motherboard and then go "lower" than it to their destinations. Even the USB header cables, power switch/LED cables/ front-panel sound jack wires (look at the 6-o-clock positition of the mainboard in the photos) immediately dive under the mainboard on their way to their other ends.
The best cases are conducive to this sort of layout, as the case he's selected really is.
If you don't have a case that's set-up for this, you can still do a lot. I like building SFF cases (small, shoebox-sized cases) for folks, and there's no room for hidden wiring channels in the cases, but electrical tape can be your friend. As I fit the mainboard and drives in and see where the cables need to go, i then normally take out the mainboard and then use electrical tape to route various wires and cables to the "floor" of the case, and then the mainboard goes on top of the taped-down wires. Those fatter bundles that can't get under the motherboard get zip-tied together and ideally connected to the chassis somewhere out of the way.
BTW, I sometimes find that the neater the cable arrangement, the harder it is to replace certain components without taking apart the whole damn system. Replacing a power supply can be a real chore on a system where I've been to anal-retentive with the cables. Twist-ties may be better than zip-ties when you expect to do a lot of hardware testing and swapping.
-Llama