Proof that the remaining 10% is worthgetting sent to the stars for here:
These are recommendations made by Tropers for Yu-Gi-Oh! GX, all of which have been signed. After a few samples, you will be able to judge whether you might be interested in the 'fic, based on who recommended it. No-name recommendations will be zapped. Nobody would back up the rec. Discussion of the recommendation is welcome on the discussion page. As such discussion is important, do remember to add the discussion page to the watchlist, if need be.
Do warn when a fanfic may head into non-canon territory. Some people just don't like it, and as we all know, Shipping is Serious Business.
This author has written a Trilogy of Next Gen Fic, the first two staring the Spin-Offspring of Yugi Motou participating in the Gx Canon, and the third(and still in progress) proper Next Gen Fic staring an original adventure. The second fic contains NSFW material.
Stories focused on the family and the friendly relationships of the cast. Plot-focused stories or light day-in-the-life stories. Pretty much anything that isn't focused on romance.
''Yu-Gi-Oh GNext by Anime Master ZERO
Synopsis: A retelling of the second season focusing on Misawa, and why he joined the Society of Light. Contains slight AU.
Comments: If you're angry over Misawa's Demoted to Extra treatment in the series, fear not. This fanfiction proves that there are people out there who care about him. This fic also provides insights on how the way that the Society gets its members is More Than Mind Control, and no character is left flat. Note that there aren't a lot of duels, though.
Timber!: Seconded. In this Troper's opinion, it told the Society of Light arc better than the canon did, and in a way that made much more sense.
LilyNadesico2: I, on the other hand, reccomend this. It's well written, the characters are actually well developed, and it avoids the wallbanger moments that destroyed the canon series in my book. Definitely worth a look.
So Far, So Good by Heleentje (there is death in this fic, and it can be violent)
Synopsis: This is set post-canon and involves mainly Juudai, Johan, and Yubel, with appearances by other canon characters at various points as Juudai travels. The general plot involves a force known as Chaos and the search for the incarnation of Good Light, which could be much closer to Juudai than he thinks, in more ways than one.
Comments: This story has now been completed and is still absolutely wonderful. The original characters are well written and believable, a rarity in this fandom, and the plot is well thought out and even more well crafted. Be prepared to have your every heartstring tugged, even the ones you didn't know you had.
Synopsis: This is poetry dedicated to Duel Academy's Kaiser...Zane Truesdale or Ryo Marufuji, whatever you wish to address him by. Criticism is allowed. Fourth part, addressing his Dragons and his brother.
Comments: Like it says above, this is a series of poems about Ryo Marufuji/Zane Truesdale that reads almost like an epic about his rise to power, his fall into darknes, and beyond. Very nicely done, and very emotional.
Synopsis: 5 years after graduation Jaden still hadn't confessed his love to Alexis & now she's getting married to someone else! Now Jaden must travel back in time reliving the awful memories and also to confess his feelings before somebody else does! Fianceshipping
Synopsis: Kamen Rider. They are masked heroes that protect mankind. Armed within the Deck, Kurogasa Kururugi ventures out to the prestigious Duel Academy as he sets on his journey to find his father and determine the path of his destiny. Henshin!
Comments: A very good read for those who want a Yu-Gi-Oh! and Kamen Rider Crossover. It starts off rather slow but it picks up speed and leaves you wanting more. Many OC involvement and many divergences from the original Yu-Gi-Oh! GX so it isn't a complete rewrite of the anime series with added characters. Season 2 is in the works.