My wife will confirm that random, unorganized wires make me crazy. That goes for TV cables, computer cables, etc. Everywhere in my home, my cables are obnoxiously clean and well organized, except... in my tank stand.
I've got a Red Sea 425XL, and it has a "dry side" of the cabinet, where you would keep your wiring. I started with the cabling very neatly routed and secured, but I could see right away that tightly bound cabling would be a definite no-go. I built a facade with a hinged door where all of the wiring is hidden behind. This way, when you open the cabinet, you see controllers (Apex, pump controllers, etc) but no cabling. Looking behind that panel, you will see an absolute mess of wiring. But that mess allows me to unplug, re-route, trace cables, etc. This seems to be pretty similar with most of the replies.
I have a background in structured wiring, and have wired up data centers, headends, home data panels, etc. These systems work with permanent cabling, but our reef tanks are another story. I think the rat's nest actually works best. I just like to hide it.