Noise can come from a lot of different things. It can be from the guitar(pickups, shoddy wiring), radio interference, cables, pedals, power supply, and the amp.
As for the pedalboard, I believe that having an isolated power supply really minimizes noise. Some pedals, especially the digital ones, don't like being daisy chained or sharing a power source which tend to add extra noise to the signal. An isolated power supply helps against those kinds of problems.
For a tube amp, having fresh tubes helps. If it's an old amp, get the filter capacitors checked as these caps tend to induce hum as they get older.
To pinpoint noise, you can start with just your guitar straight into the amp. Then slowly add pedals, cables, power supplies, etc. so you'll see which ones are noisy.