Well I guess I'm not sure I understand your question.
For a long time I was a big fan of zip ties and split loom. It does indeed look nice when it's finished but if you ever want to change something better have some cutters handy and a bunch of replacement zip ties.
When I built my basement theater
I decided to use Velcro ties
instead. They worked fantastically. They're easy to use, hold very well, and are reusable.
If you're asking how do you know which wires are ok to bundle together that's going to depend on a few variables. As a rule you don't want to bundle anything carrying power with anything carrying signal. In other words you don't want to bundle your component video and power cables together. If your power isn't clean you CAN induce 60hz hum on the signal wires. In audio this comes across as a huming. In video it comes across as a rolling line in the picture.
With optical cables like TOS/LINK you want to avoid kinking them at all costs and doing so can cause the fibers to break and stop carrying the signal. Make sure you leave enough slack to have a gentle bend in the wire as opposed to a sharp kink. Think of it like a water loop in your PC. You wouldn't want it to have a 90deg bend, would you?
Speaker wires are ok to bunch together. Just make sure the weight of the bunched together wiring isn't so heavy as to pull the cables out of the rear of the AVR. I've seen this happen with 7 channel systems and heavy gauge speaker wire. While we're on speaker wiring, I can't recommend banana plugs enough. When you start getting connection dense on the rear of your AVR with 5.1 and 7.1 systems using those little screw down terminals can be rough. Banana plugs eliminate the need for all of that.