Mamoru Oshii studied in christian school and in his personal works of the late 80 and 90s he exploits many religious and philosophical themes. His surreal 'Angels Egg' full of biblical symbolism. Also his full length 'Ghost in the Shell' movies are definitely fulfilled with christian motives.
I'd also recommend Satoshi Kon's 'Tokyo Godfathers'. It is wonderful Christmas story with Dickens motives and wonderful Kon's visuals.
In my opinion, Yasuhiro Yoshiura's 'Eve no Jikan' have obvious reminiscence. I mean, androids as a persecuted minority with digital limbs above their heads is quite literal.
While Watanabe's "Sakamichi no Apollon' not christian per se, religious background of two of the main characters plays big role in plot.
And, speaking about elephant in the room, 'Neon Genesis Evangelion'.