lets run those wires!!!!!!!!
My take is - Everyone is right so far on this thread. Where to run and where not to run wires come with a lot of installer experience over the years finding out what works and what doesn't in the real world. From a practical application theory point of view the best advice is (I stress the word advice):
Speaker Cable: keep them as far away as power cables or other electrical devices in the boat. Yet, this is often times not possible.
Low Level Signal Cable (i.e. RCA's): Same information applies as above. Some of the better cables on the market will be shielded or even triple shielded to protect the dielectric against radiated (Radio Freq) noise or pulse width modulated (power supply) noise.
Power Cables: Lets face it, these guys can be a great source of noise generation. Not because they are unshielded or the like but because the power they carry is dirty unto itself. Looking at this on an oscilloscope would make people go wow! Yup! That's noise! Often times these cables get blamed for noise due to the electronic device grounding issues - i.e. amplifiers, signal processing, cd players or even speakers themselves!
With all this in mind, lets talk about ground issues, loops, and problems. Often times this is the very heart of noise issues or performance degradation and with a little planning they can all be avoided. someone mentioned boats seem to have less ground problems that cars. It might seem that way but the reality is they have less active system (read audio landmines) than a vehicle has. They do share the same common issues however. The most common ground problem is actually a physically bad contact between common chassis and the electronic device. In boats often times you can locate the common area where most of the devices run to. My advice is use it!!!! Because what happens in a ground loop (i.e. audible system noise), your actually hearing the +/- differential between the grounding of two devices that are active within the system. Everyone follow that? Best way to avoid all those headaches is use physically central contact/connection point.
Now this isnt to say that even if you do all this that your system wont have noise issues.... other things can happen and they do but you have to address them on a case by case basis. Hope this helps :)