The worst noise I've found with pedalboards is usually the power supply. If it's not an isolated power supply, or if it's mounted close to a susceptible pedal, it can cause a lot of noise. It's not a sexy thing to spend money on, but it's kind of like the foundation of your house.
That being said, I used to make my own cables (someone mentioned Redco; I've given them a lot of business!), but really prefer the flat, premade cables by EBS. I have some of Warwick's Rockboard cables as well, but a couple of them have popped the covers off, so I'm sticking with EBS.
Warning!
\rant-on
On a separate note: why are we still using 1/4" plugs designed for ancient telecom systems? If we could move to something else, not only would the cables be less bulky, but the pedals themselves could be much smaller without that much plug penetrating them? Maybe use strat-style jacks on pedals to make the pedals smaller? Sorry, planning a pedalboard and questioning the current state of things.
\rant-off
Enjoy the journey!