Second to the Layers palette, I find Custom brushes to be most commonly messy habit for digital painters. How many brushes do you have? What's your system for organizing them? This video shows my preference, and one cool alternative (linked to the right.)
If you have another system, we'd love to hear about it in the comments!
Note: In this video I say "Blender Brush", when what I meant to say was "Mixer Brush".