Literature is often full of symbolism: words, symbols, or other things that evoke images or allude to outside influences without the authour having to specifically mention the meaning of the symbol. For example, heroes in certain stories often share similar traits, most likely due to influences on their characters from previous tales. The Bible, being a well-known piece of literature (at the very least, it is a book) is often the source of many influences that modern-day writers draw on, particularly with heroes in certain kinds of tales being required to sacrifice something - sometimes their life - to save the world. It's obvious that Hoshino Katsura is drawing on at least one of those tales - Noah's Ark - for D.Gray-Man, but for a story set in an Order under the control of the Vatican, there is, as one of the posters here (=P) has commented, remarkably little mention of Catholic beliefs and figures in the story.
However, we know Hoshino does her research, and there are a few things that stood out right away about how she might have woven things into the story, so I did a little thinking and realized that there are plenty of allusions to Jesus... within the characters, particularly Allen. The most obvious fact is that his birthday is also on Christmas, but, like Jesus, the actual date and year of his birth are unknown. Allen also has no known parents but was raised instead by Mana Walker, who adopted him (since Mary apparently conceived Jesus without the help of a man - virgin conception and all - Joseph would technically not have been Jesus's biological father, either... of course, that's just the legend, but going on that-). There's a chance that Maria was involved in that, since her name is, of all things, Maria. It's also interesting to note that Mary is famous for the Magnificat, which is a song - Maria the Exorcist is apparently a singer.
Then there's the incident that happened when Allen was twelve - Mana's death. That famous story of Jesus in the Temple (the "Finding in the Temple") occurred when Jesus was twelve. Important age, huh~ Another interesting person, Joan of Arc, began to have her visions at the age of twelve (possibly like Allen getting his cursed eye and being able to see and hear the souls of akuma).
The first story involving adult Jesus in the Bible is his baptism, where he is revealed as the Son of God. Allen makes his first appearance many chapters before a similar incident, but he isn't completely taken into the Order until he's checked by Hevlaska (certainly a chilling feeling!). That's also when Hevlaska prophecies Allen's future as a "Time Destroyer".
On to something really important~ Jesus was said to have twelve apostles, right? On both the sides of the Order and the Noah, there are thirteen of Exorcists and Noah each besides Allen himself. For the Noah, Skin is apparently dead, so there are twelve Noah. There are thirteen Exorcists, so it's possible - and likely - that one of those (Bookman? Sokaro?) will die and leave thirteen Exorcists, including Allen. Interesting numbers, hm? One of the apostles also betrayed Jesus - Judas could be an influence on Chaoji, who doesn't like Allen and would probably not hesitate to betray him to, say, Leverrier.
As for the betrayal, Allen is already being suspected by his allies: the Order, who want to arrest him for heresy. Joan of Arc (I mentioned her above) was also tried for heresy (and executed, although she chose to wear men's clothes to prevent being assaulted in prison and that's what apparently led to her conviction and death). Jesus died in April; the time in DGM is currently winter (probably around early to mid-December), so a confrontation and conclusion to the battles, or even a trial, could very well be in the spring. Allen has already been "resurrected", too - he died and came back to life, although not in a very dramatic way. =P He did, however, have a certain woman who is very close to him crying over his body~ It's possible that the same will happen after a final battle, since we all want a happy ending.
Back to the Apostles thing, Lenalee could be a parallel of Peter in the story. Peter ended up being the closest Apostle to Jesus, later becoming the first Pope. Simon Peter, along with his brother, were the first two to become Apostles; Lenalee and Kanda were the first two Exorcists to be introduced after Allen and met him around the same time. Lenalee also has shown an ability to walk on water; this could be a Jesus thing (because of Lenalee and Allen being the Heart, perhaps?), or Wikipedia says that Peter was the only other ever taught to do such a thing. As far as we know, Allen can't, so... well, anyway. (Jesus did perform miracles of raising the dead. This could be related to Allen bringing back his friends in the Ark, who were gone if not dead, or not.)
Komui seems to play a role similar to Pontius Pilate; he has a role of authority and is involved in the watching - and possible eventual trial - of Allen. Like Pilate, he doesn't believe Allen is guilty, but will likely be forced to do the will of those who have power over him.
Finally, the less specific references and allusions. Allen's "Crowned Clown" invocation is actually written in kanji as "God's Clown". The second part is the same, but on one hand, you have the reference to God, while on the other, the mention of a crown (Jesus claimed to be the King of the Jews. Allen doesn't seem to be any king, but he's got a crown). Additionally, clowns were associated with outcasts of society, such as prostitutes and lepers; these were people who Jesus also associated with. Clowns also had freedom of speech as they were considered to be fools, and could therefore say controversial things. Allen is generally a nice person who displays a remarkable capability for forgiveness: he doesn't hate akuma or Noah despite their apparently evil deeds and wishes to heal them. He even treats people like Kanda with respect, even if he's a little more than willing to argue with them. Still, Allen is clearly just a human, and has human weaknesses and worries like everyone else.
Something important that actually inspired me to make this thread and that I want to emphasize: the Noah have a circle of crosses on their head. This is very likely to be an allusion to the Crown of Thorns that Jesus wore before being crucified. Really, it's just too much like it to be coincidental, particularly since that crown is such a famous symbol. Another of the stigmata is the bleeding of the hands or wrists (from Jesus being crucified); Tiki's hand was bleeding when he was transforming into that super-Noah.
And as an afterthought, Kolox and Reinard were saying Lenalee doesn't dress like a nun - actually, new nuns cut their hair very short, as Lenalee's is now. They also wore white (Lenalee's current outfit is white, although she usually does wear black).
I've probably missed a lot, or didn't think of plenty of things, so please feel free to add anything you've thought of here. It's possible that some of this is coincidental, or that Hoshino herself didn't think of Jesus specifically when adding it, but there just seems like too much to ignore. Sometimes, it's surprising what the authours thought of~