It's often been said that from a practical standpoint, this doesn't really matter, because the two are interchangeable depending on which side of the paper faces up. But I think it's important-- for asymmetrical designs, the crease pattern should produce a model with the intended chirality; and if the creases are in the wrong direction, we'll get a left-handed model instead of a right-handed one. Also, often people will assume that the crease pattern is viewed from the top or front side of the model, if there's a clear correspondence to that, so when we draw a CP we should be setting them up to get what they expect. The crease pattern is conceived as an orientable surface, and therefore the parity of the creases is not interchangeable and shouldn't be ambiguous.
Here's a list of reasons why I feel the colors I use are more appropriate:
- Red is a bright, active color, and pops out at you, especially on a computer screen; mountain creases are more visible on a sheet of paper, and drag the paper forward towards the folder. Blue is a calm, low-key color, and valley creases are less visible on a sheet of paper, and recede from the folder. So from a visual standpoint, it makes sense.
- Red light has a longer wavelength; "redshift" is the phenomenon where light waves are stretched towards the red end of the light spectrum because their source is moving. The opposite term is "blueshift" in astronomy. The fibers on the mountain side of the paper stretch apart; the fibers on the valley side are compressed. Red/mountain and Blue/valley would be consistent with existing scientific terminology.
- Mountains have a ridge of rocks on the top; valleys have a river running down the middle. Rocks are represented by brown or gray, and water is represented by blue, in all cultures I'm familiar with. Mountains can also be volcanoes, which are definitely associated with red. Seems like the colors should match up.