PEX is great. That being said, here are my AHA moments:
Use the clamps and the special tool to clamp the PEX to fittings. DON'T use the copper crimp rings. If you crimp the copper and it leaks or if you decide to change the fitting, you have to cut the PEX and throw out that fitting, because the copper can't be pryed off.
Test your lines before you cover them up and use as few fittings as you can. This seems self-explanatory, but easy to overlook in the excitement.
Bending the PEX and using one of the "bend holders" will help maintain better flow than a crimp-on elbow, and fewer joints.
Buying both blue and red will help you identify lines later on. Obvious, but worth mentioning.
Adding ball valves (never gate valves) will help isolate runs later on if the need arises.
They make PEX fittings to attach to everything, including shower valves, so I would recommend replacing all of your copper rather than attaching to it.
Don't run your PEX in ways that they can leak or run into any electrical or electronic equipment.