As long as the N##### is properly displayed, then anything goes. Many homebuilders get really creative with their paint jobs.
Most of the time you will be selling the plane before it needs another paint job. So, putting a really wild paint job could easily reduce the resale value.
Also adding too many layers of paint can really reduce the useful load. Paint weighs about 8-10 pounds per gallon, and a light plane take sevreal gallons. Adding two or three coats of base, and then several diffrent colors can easily add up to 50-60 pounds.
Most planes are painted white, since white dosen't absoarb heat like dark colors do. Light colors also are easier to spot. ERAU has all their planes painted with "invasion stripes" on their wings to make them more visible.