I can think of 3;
Panty and Stocking: Angels sent from Heaven fight ghosts and demons
Gabriel Dropout: Angels sent from Heaven learn about human life by attending high school.
Ghost Stories (watch the dub): Highschoolers fight ghosts and demons through the power of our Lord and Saviour Jesus Christ.
In the Beginning is an anime that follows the Christian old testament up through the birth of Jesus.
There's also Superbook about 2 kids and a robot who time travel to bible times get involved in the biblical events.
Samurai Champloo has Christianity as part of its story as it develops.
Saint Young Men also might be good to check.
Chrno Crusade sorta I guess. You'll tend to see more Catholic motifs than Christian in anime. Even then it's not usually explicitly using Christian or Catholic themes, more just aesthetics.
