The Bogatin book looks pretty good, and you can begin to see the complication here. The guy has PhD, 30-years experience in the specific area, and 300 publications, plus the book is 587 pages.
That being said, it's certainly possible that a few interventions will help the problem greatly. There are at least 3 means of interference:
- conductive - via direct wiring, where inline filters should help.
- inductive - short-range pickup due to wiring loops, such as connecting everything using silly Arduino jumper wires, and where the solution is to shorten the wires, use twisted pair to reduce the loop inductance, use shielded wires, use differential-signalling, etc.
- radiative - direct electromagnetic transmission at high-frequencies, and where shielding and physical separation are the first steps, followed by hi-frequency filters on I/O lines.
The problems also get compounded when you have signal wires coming to I/O pins via high-impedance pathways, eg from non-terminated open-switches, as they act like antennas for picking up noise. So, it's best to keep signal pathways low-impedance, eg always have moderately low-value terminating Rs to gnd on I/O pins.
As you'll notice, our Arduino and RPi boards essentially have none of these features designed in.
EDIT: forgot to mention, the guy has a website with probably a lot of useful information (unfortunately, the place is all about making $$$):
http://www.bethesignal.com/bogatin/You can see the topics he covers here:
http://www.bethesignal.com/bogatin/product_info.php?cPath=88&products_id=833