Just in the books I have, I've read these strategies for organizing your palette:
1. Opaque paints on one side, transparent on the other.
2. Warm colors on one side, cool on the other.
3. In spectrum order, regardless of these other properties (i.e., white, follow the color wheel basics).
4. Earth tones first, then spectrum colors.
This is what Mitchell Albala says in his book "Landscape Painting:"
The palette is more than just a place on which to squeeze out colors. It can be a roadmap for thinking about color and color mixing. Always lay out your pigments in a consistent and logical order; this will allow you to work faster and smarter. Avoid the "spotty palette syndrome," with colors randomly placed in different spots each time you paint.Uh-oh. Guilty as charged. Something else to work on -- curing my "spotty palette syndrome!"