I believe I have found the inspiration behind the paintings in the church in Silent Hill 3- some of the religious works of Michelangelo Merisi da Caravaggio. Not only the almost baroque lighting style, but much of the imagery and even poses carry over astonishingly well.
Going in the order of the paintings...
Origin shares a pose and a good deal of composition with the Conversion of St. Paul.
Origin:
the Conversion of St. Paul:
The case for Creation is slightly more tenuous, but I noticed a similarity between the being to the left of God and several depictions of angels in Caravaggio's pieces. There's also some examples of the use of red cloth.
Creation:
the Seven Works of Mercy:
the Martyrdom of St. Matthew:
St. Matthew and the Angel:
Salvation shares a lot of thematic imagery and at least one pose with Madonna of the Rosary, as well as very similar compositions.
Salvation:
Madonna of the Rosary:
Promise is possibly the closest to what may be the inspiration- the Death of the Virgin. The compositions are almost identical, most of the elements are carried over.
Promise:
the Death of the Virgin:
I haven't found anything that looks like Birth or Faith, but the rest seem similar enough to be worth pointing out.