Master of Darkness is a great design. To me it just edges out Ninja Gaiden. I actually chose Ninja Gaiden first, but then as I continued to look at them both, I had to admit that Master of Darkness has a more striking overall composition. And the crazy skull sticking out its tongue really drove the point home - this is, as our German friends say, the programmed insanity.
All are great covers but I'm going with Master of Darkness as nostalgia gives it the edge. Ninja Gaiden is a very close second. I have a feeling both covers where done by the same artist (the games were programmed by the same people).
Ghouls n' Ghosts is a great cover and holds a lot of nostalgia for me but it isn't quite as detailed as the aforementioned covers.