I don't know if there's one best practice, but the following might be helpful:
- Limit the voltage on input pins to 5.5 V maximum.
- Do not shorten IO pins.
- Use pullup or pulldown resistors when conecting switches or pushbuttons.
- Respect the current limits (for each pin and in total). Use resistors.
- The Arduino is just the brain, not the power station. If you have to drive higher loads, use simple transistors, Darlington arrays, etc.