The most common is Aotake Blue. For this, I first paint the surfaces in aluminum. After it has cured for 48 hours, I spray a mixture of Future & clear blue (both Gunze Sangyo & Tamiya make this acrylic color) over it to simulate the clear, tinted protective coloring.
Aotake green was also used. This can be simulated by substituting clear green instead of blue in the above example.
Some wheel wells (particularly late war) were painted in the undersurface color (Mitsubishi or Nakajima Navy Gray).
There are MANY walkaround pics of museum pieces & relics on this page.
http://j-aircraft.com/walk/walkarou.htm
Hope this helps.