A huge portion of laying out a board is wiring it. There have been plenty of layouts I've put together that fell apart when I started to layout cables. Even the smallest, slimmest plugs take up space between your effects.
The first way to keep it as clean as possible is to use custom length audio cables. There are a few solutions available for custom cabling, but they fall into two main categories. Solderless and soldered.
I'd say George L's is the most known brand in the solderless cable area. It's what Corey has used to wire his board. They are remarkably easy to put together and are very small. There are other brands too like Evidence Audio and Planet Waves. Evidence Audio being the cable used in the Radiohead video recently.
Soldering your own cables is considerably more difficult. It requires some tools and some knowledge of how cables are constructed. For my board I use a spool of Mogami Cable with Switchcraft plugs. I love the look and feel of these thicker heavier cables and plugs on my board. Thinking about soldering your own cables? Invest in a cable tester. It'll make your life much easier.
Power cables are also a concern. If you're using the Voodoo Labs pedal power (or most of the standard power supplies) Voodoo Labs offers cables in many lengths including custom and make your own. Word of caution: the make your own cables require soldering. It's recommended to keep the power cables and audio cables running perpendicular to each other. This is so the audio cables don't pick up the noise from the power. This isn't always the easiest thing to do, but is recommended.
Depending on the board you are using you may be able to run cable beneath the board. This is great with Pedaltrain boards and allows you that much more space. It also keeps things quite clean. Corey has his power supplies beneath his boards so all his power cables go below. Keeps it clean and separate.
A huge portion of keeping a pedal board well wired and clean is cable ties. I use small zip ties to pull everything together and little cable tie mounts that hold everything in place. This is usually a great final touch and can take a board from good to great.