I also leave all my systems hooked up. There is not much i can do about the 50 cables behind my tv, so i use velcro cable ties for the audio/video cords and power cords since those consoles don't move. Consoles that i need to move out to play due to short cords (N64, NES, PS2, Dreamcast), i will have an extra set of audio video cables that i can plug straight into my converter.

For controllers, i am still battling that. I used to wrap the cords in a oval shape and them velcro strap them, now i don't do that anymore since it's not good for the copper. So i put 2 controllers in plastic gallon bag with their cords loosely wrapped in a circle. Then i put those bags in those fabric bins for my 6x6 cube storage thing.

I think as time goes on, i may try and get more retro wireless controllers, but at the moment i don't play those consoles that much, so it's not worth it at $35-65 per controller.