I would use the grommets in places where you don't want the wire or tube to shift laterally (through the hole) - i.e., where you want to actually hold the wire/tube. Snap bushings provide protection from chafing also, but allow the wire/tube to move laterally. Of course, you can always RTV the snap bushings to keep things from moving or to seal things up (such as on the firewall).
I used a lot more snap bushings than grommets mostly because they take up less of the hole. You can use a smaller hole in the structure to carry more wire. They're lighter weight, and I'm guessing they'd be less prone to degrade over time due to heat, ozone, etc. I did use a few grommets, mostly the small ones where I only had a wire or two, or I didn't have enough clearance for the extra length of the snap bushing.
In my recent refit of my RV-4, I replaced a bunch of old cracked black rubber grommets with red silicone grommets from McMaser-Carr: http://www.mcmaster.com/#1061t63/=19brcw