IMHO what is generally lacking from application notes and example diagrams are the components needed for EMC compliance. Too many are hiding behind the phrase 'it depends' while there are simple recipes you can follow. For example: series beads and TVS diodes on ethernet lines, a common mode choke and (again) TVS diodes on USB lines, a common mode filter on a DC power input. Now everyone has to reinvent the wheel for themselves.
But... those are all terrible examples?
Well, the last one, CMCs on power supplies, is fair game. But whether they work or not, depends on the rest of the circuit.
The biggest downside is that EMC is more holistic than usual circuit analysis.
You have to be willing to see your circuit as a much smaller simplification.
Riddle: when are mains hot and mains neutral shorted together and effectively identical?
Answer: when you put a fuckoff huge capacitor between them, so the impedance from hot to neutral is very small at higher AC frequencies. At HF, you can reduce the mains input to two connections: mains and ground. Now the common mode circuit is much more obvious: it's a series inductor and some parallel capacitors. And the capacitors better not be parallel from a noise source, but shunting to ground.
Using ground planes or supply rails as Faraday cages provides similar reference and optimization in other circuit areas.
The most often-repeated mistake is adding impedance where it doesn't matter, or where it's worse. Example: a cable in free space, acts like a large ratio coax transmission line, so has a high transmission line impedance. Adding a ferrite bead in series, even a large one (~300 ohms?), provides only a modest reduction in noise (~6dB). (This is, however, an ideal amount to dampen resonances on the line, which can have a big impact on susceptibility, and on emissions at "unlucky" frequencies.) Whereas if the far end, or both ends, of the cable were grounded, you get an impedance divider and much more reduction (>20dB easily). Another example: adding a ferrite bead to a ground connection (an oft repeated mistake on USB connections, even in appnotes!).
Tim