In fact, even though the ceiling takes most of the fame, my favorite painting was Michaelangelo's Last Judgement depicted in the altar wall:
http://en.wikipedia.org/wiki/The_Last_Judgment_(Michelangelo...
The later-added fig leaves and robe parts do stand out which I thought was a shame. Lots of art in the Vatican museum have private parts which have been broken (in statues) or covered/painted over.
Another impressive point that stands out is that the ceiling is mostly flat. The painted arches and columns give it an amazing 3D look.