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These are recommendations made by Tropers for D.Gray-Man fanfics, all of which have to be signed to stay on the page. Feel free to add a fanfic of your own to the list, but remember to use the template found here.
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Pairing(s): Diverse. She even has a collection that focuses on as many different ships as she thinks plausible.
Not only is she excellent at characterization, she often writes about characters that the fandom forgot. If you're interested in reading about everyone from Anita, to Ease, to Fou, as well as the main protagonists, look no further. Picaropicara provides an engaging and frequently poignant look into everyone's lives.
You can also find drabbles on her livejournal: 
Pairing(s): Almost entirely Kanda/Allen, but there's also Kanda/Allen/Lavi, Tyki/Allen, Cross/Anita, and Tyki/Lavi.
Sutlers sugar-coats nothing, romanticizes nothing, and still manages to make completely beautiful fic. The basis of her fic is kind of like no one is perfect, everyone fails in some way, but the best part is when people work to be together or at least have some semblance of happiness. Her characterizations are awesome, everyone seems like a real person. She has great control of the language, especially when describing severe environments. Also there is lots of sex.
Pairing(s): Hinted at/follows through with Pairings already in the respective Series.
Synopsis:There was the softest sound from the window; he spun to look. He found, much to his alarm, a figure cloaked in black crouching down and balanced precariously on the sill. "I did not expect to run into a exorcist here."
Comments: This is written like a book, the Author stays true to all the characters and develops them fantastically. It follows through the manga story line and the 7th Harry Potter story line and merges them in a wonderful way. Best fanfiction I've ever read.
Pairing(s): none though there is that ridiculously funny part where Lavi is dressed as a girl and a young man takes a fancy to him
Sypnosis: This is the story of Bookman and how Lavi became his apprentice. It follows their hardships and adventures together throughout the years until they reach the Black Order.
Comments: The characterization is awesome, the plot is GREAT, you even get to see Cross Marian and some other characters make an slight appearance. The comedy is wonderful, not too much but just enough in the right places that really remind you of the original manga. This is a must-read for all Lavi and Bookman fans. Too bad it's been dead for a while.
Sypnosis: Mana Walker is 36 and leading an average life, living in a small apartment, lusting after his secretary and hating his job. His life will be changed forever when he finds a boy hiding in an alley.
Comments: I can't believe this isn't here yet. This story is quite legendary, having inspired other authors to create their own versions (see Bookman^), a bunch of one-shots, a sequel, and even one for Komui. The fic is basically about how Mana met Allen, and how their relationship grew from a poor abused boy and an office man to a loving father and son. It even has a sequel, although I hate that one for taking the M rating to a whole new level.
Synopsis:A war-torn Allen and the few he can still call friends are sent to the past during what should have been the 'final battle.' Though Allen tries changing this past, other forces appear... along with an almost forgotten prophecy.
Comment: Epic battles. Complex character relationships. Equally complex and emotionally engaging characters.
Stories focused on the romantic relationships between the cast.Forget Me Not by NerdInAWord
Recommended by syriiak
Synopsis: When Krory forgets everything he ever knew about his past thanks to an accident, he grows closer to a certain someone else: a certain nervous, apologetic Exorcist. But what will happen to their relationship, as both friends and lovers, when he starts to remember Eliade?
Comments: A wonderful fanfiction about a pairing that is hardly shipped. It's well-written and beautifully made. There is a bit of everything in this: humor, adorableness, and some tears.
Synopsis: Alternate universe. Injured in a war, a mute Kanda finds himself being treated in an old castle that's been converted to a field hospital. Soon he is joined by Lavi, who is deaf, and Allen, a young soldier who, now blinded and lacking an arm, must find a new purpose.
Comments: This fic is beautifully written, with a focus on character interaction.
Synopsis: His vision blurry, the movements of the body situated in his lap were slow and smooth, the expanse of skin down between rolled up sleeves and white gloves made him think of cocoa powder and milk poured and hardened on bone. Dub-con.
Synopsis: AU: January 2nd, 1985; "Wanted- Band member. Must have patience." Allen Walker's gonna need a whole lot more than just patience to keep up with their world of music and life. :Kanda Allen, Lavi Allen
Comments: Yes, it's AU, yes it's the 80's, but it is so worth it. It's hilarious in the beginning, and only gets better. Later chapters are more intense than the previous ones. Lots of swearing and mentions of drug use.
Synopsis The Order must put up with its unwanted, new ally the Fourteenth; his charms and attempts to pacify the Exorcists regardless of his role in Allen's death were all in vain...for a while. Then we find out that Allen isn't really dead, and then later comes the huge bombshell of his parentage. Slight AU. Set after L4 attack on HQ, before Timothy and Child Thief.
Synopsis: "If you cannot stand to remember what you have lost, give to me your past and I will blank your slate. In return, I will use your body to do His work. Just don't get too attached… because our relationship cannot last. And do not forget… I love you."
Comments: Don't let the fact that this has an OC turn you off. The character has her faults, and fits in well with the D. Gray Man cast. Her romance with Komui is believable; it takes a long time to develop, and even then they have their problems. This isn't just romance, either. It has a very developed plot, one that sticks to canon but isn't afraid to stray away a little. Better yet, it has an update schedule the author always sticks to. So, even if you don't like OC fanfiction, give this one a shot. It's well worth it.