This article is sort of a response to the question 'What do all thosecrucifixes in manga mean?' I'm writing from the perspective of a (former)cradle Catholic and a (still) non Japanese and I can only say how the Japanese use of Christian imagery looks to me. If any practising Christians or Japanese disagree with my views, they're cordially invited to discuss the matter in email with me.
My view, I will say at once, is that they don't mean much of anything, as we westerners count meaning. That is, the artist who draws her characters in a pose taken from Michelangelo's Pieta probably isn't drawing parallels between Christ and Izumi and Mary and Koji. (Or is it Christ and *Koji* and Mary and *Izumi*? Christ and Mary I can tell apart, but Koji and Izumi give me trouble.) She isn't implying that Izumi (or Koji) is the son of God, or born of a virgin, or consubstantial with the Father and the Holy Spirit or any of that obscure doctrinal stuff. She isn't implying that dead Izumi has any of the characteristics of Christ as Redeemer- that his death has somehow provided salvation for mankind, or even man, or even Koji. No, it's simpler than that.
She draws Izumi in the pose of the dead Christ because it looks good.As many Renaissance artists recognized, it's a neat way to draw a nakedyoung man. The other way, if you're a Renaissance artist, is to turn himinto St. Sebastian and stick him full of arrows. The Japanese like thatone too. My copy of Confessions of a Mask, Mishima's semi-autobiographicalnovel, has the author stripped to his fundoshi (a Japanese loincloth) and pierced with an arrow or two. But the Pieta pose gives you two bodies tobalance against each other, which makes for a more satisfying composition,and provides some free emotional 'plot' by suggesting that the Mary-figureis grieving for the Christ-figure.
In other words, the deep significance that people with a Christian background attach to Christian symbolism isn't likely to be picked up bythe average mangaka in the street. To get a little airy-fairy here, westerners have a long tradition of prizing the content over the form. We say, 'It's not how it looks, it's what's inside that counts.' Hence our symbols- whether swastikas or crucifixes- are actual *symbols*: they mean something beyond their surface appearance. They carry all the baggage of the ideas and actions that have been associated with them through the centuries.
Japanese are more likely to go for 'First impressions are lasting.' In Japan, the way a thing looks is the indicator of its quality. The surface appearance is what counts. So, when you go to the Meiji Shrine to see the irises on a Sunday in June and watch the ranks of amateur painters out painting the irises, you'll note a disproportionate number of berets. A real artist, as we all know, wears a beret- just as hikers wear knickerbockers, heavy woolen socks to the knee, and felt Tyrolean hats with a feather tucked into the brim even in the steamy depths of summer. Yes, people do go for walks in the mountains in jeans, but a proper hiker looks like a German mountain climber from the 1890's.
This cultural factor means the Japanese are quick to pick up the identifying markers of things. They can, and do, reproduce the surface 'icons' of a subject but generally without thinking that these surface markers may have a meaning beyond what's immediately visible. God knows what a real Rastafarian thinks of the Japanese who spend hundreds of dollars at the hair salonto turn straight hair into frizzy dreadlocks, at specialty clothing stores for pure Made In Jamaica wear, and in tanning salons to turn gold skin into as-brown-as-it-goes. They're into the look, not the religion.
To take a secular example, many people have asked me about the meaning of the roses that are drawn in such profusion in the back of many manga scenes. They don't have a meaning in the sense that roses symbolize passion in the west and lilies symbolize purity etc. Roses don't have a deep meaning in the Japanese system (unlike lotuses and chrysanthemums) though the Japanese are culturally aware that they do in the west. So my guess is that roses in a manga are mostly there because they look good and partly because of some vague associations- romance, sweetness, what have you. Shallow meaning, if you like, not deep meaning.
OK- back to our crosses. Crosses work the same way. They're a neat design. They have associations with Christianity- which is not the belief system of any Christian religion so much as the look of the Christianity that the Japanese are familiar with on their own turf: 16th century Catholicism. 16th century Catholicism, be it said, was no slouch when it came to putting a look together either. The Protestant Reformation had attacked, among other things, the 'look' of Catholicism- the statues and crucifixes and paintings, the music and incense, the cult of the saints and the virgin. Protestantism was all for Man and God and nothing else. Catholicism responded by playing up all the trappings the Protestants had taken aim at- making a big thing of its saints, pushing the cult of Mary, building bigger and gaudier churches with more statues and gold and lights. St.Peter's Cathedral dates from this period, and the whole baroque movement in art. Say no more. The 16th century Japanese daimyo who decorated their tea ceremony chambers in gold leaf met the gold-encrusted Spanish Catholicism of the time, and it was love at first sight.
A pity, perhaps, because Christianity is in many ways a bad match for the Japanese mindset. As has often been said, 
the Japanese are more comfortable with here and now realities than with abstract concepts. Take the Redemption- one of those mystic things Christianity can't explain. The Catholic line is that the human race fell into a state of sin because of the sin of Adam and Eve, whatever it was. Maybe they ate an apple; maybe they ate a symbolic apple; maybe eating the apple, whether real or symbolic, was a mark of turning from God by doing something they had been forbidden to do; maybe the real crime was turning from God and had nothing to do with the apple if it was an apple. Whatever. The sin of Adam and Eve infected all their descendants (the doctrine of original sin.) All human beings are born into a state of sin: we're guilty before we've done anything but draw our first breath. But fortunately God chose to be born as a man, Jesus Christ, and chose to die as a man; and this death merited enough grace to wipe out the original sin of the human race. Not that the forgiveness of original sin is automatically given when you're born. You have to apply for it in baptism, or your parents apply for you, the same way they see you get your six month booster shots.
Still with me? The Japanese had and have a problem understanding this abstract part of redemption: the notion that God's own sacrifice was what provided, shall we say, the energy to fuel the salvation of the human race. They had to recast it in cultural terms they could understand. Christ was the Son of God, good. Christ's Father told him to go and die, good. (Japan was very Confucianist at that period. Confucianist fathers can do these things.) Christ, good obedient samurai son, went and died. Christ's Father was so pleased that he forgave the human race their sin. Luckily the Jesuit and Franciscan missionaries never managed to overcome the language problem entirely, or they'd have had to deal with the fact that most of their converts were practising heretics.