Assuming the noise you're getting is due to ground loops (and not a product of shitty PSU in the pedalboard or just being picked up by the guitar)...
1. Break the loop by galvanic isolation of power grounds
If you have DIY skills you can make a pedalboard with separate transformers for each pedal. That breaks the ground loop you get by daisy-chaining the power connections.
http://www.geofex.com/article_folders/spyder/spyder.htm
There may be a commercially available product with a similar arrangement.
2. Break the loop by galvanic isolation of signal paths
Involves putting signal transformers between the pedals. Expensive, less practical, I mention it only because it's possible.
3. Minimise the loop area
With the arrangement you have now, the best you can do is to minimise the loop area, which means running the signal and power cables along together. Wrap the power cables snugly around the signal cables.
This increases the noise coupling between power and signal wires, but if your signal cables have good braided shields it shouldn't hurt much, and it will greatly reduce the amount of noise picked up from external sources by the ground loop, which is likely to be the lesser of the two evils here.
4. Minimise ground resistance
Alternatively, a very heavy gauge parallel earth connector could be run between the pedals' chassis, and to the ground used by the amplifier. Ensure there is conductivity between the jack sockets and the pedal chassis.
This puts near-zero resistance between all the grounds, so that any EM-induced AC currents in the grounds will produce near-zero AC voltage (as per Ohm's Law).
Preferably use a ground plane or grid made of aluminium (or copper (varnished or coated), or better yet silver, or steel if you have to) with the pedals on top.
Ideally all the cable shields will be bound around 360 degrees to the jacks so there are no gaps for interference to enter through. Good luck finding jack plugs which are designed for this though.
...and try not to squash your cables. The effectiveness of the shield is greatest if the cross-section is circular. Deforming the shield is a no-no.
