Proof that the remaining 10% is worth stomping over Tokyo for here:
These are recommendations made by Tropers for Fan Fics, 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 sexual or non-canon territory. Some people just don't like it, and as we all know, Shipping is Serious Business.
A great attempt at creating an Adaptation Distillation of the entire Godzilla franchise, even featuring many monsters from non-Godzilla Toho films (Like The Gargantuas, Orochi and the Mantango), featuring a pretty cool story behind it all; which manages to merge the many Godzilla continuities and even add in a few bits of its own, and excellent artwork to back it up.
Many stories, mostly set in a continuation of the Heisie Continuity and often dark in tone. C. L. Werner is an old school fan author who has professional credits to his name and it shows. Lots of monster battles, well written but definitely darker in tone than most of the films these are based on. Godzilla vs. Cthulhu and Koumajutsu: the Coming of Bagan stand out as the Darkest I've ready.
Take Godzilla Neo, add the sensibility of Batman: The Brave and the Bold. Featuring tons of excellent Mythology Gags and Continuity Nods, some excellent character designs, and a whole load of Crazy Awesome (Godzilla uses Anguirius as a MACE). The revised characterizations and concepts run the gamut from fun and silly to genuinely terrifying, and the love for Godzilla and what makes him work is all over this. Cross-posted on several sites, it achieved something of a legendary status, but many of the notes are now Lost Forever. It has been known to induce powerful depression in people upon their realization that the show will never exist.
A creepypasta written by Cosbydef about a young man named Zachary who receives a copy of Godzilla: Monster of Monsters from his friend. While replaying the game however, he is encountered by bizarre and un-worledly imagery and a complete re-design of the Game's mechanics and gameplay. During the course of the story, Zachary is continuously haunted by a malevolent entity known as Red, "the Hellbeast", who mentally tortures Zachary while trying to hunt down Godzilla and Zachary's playable monsters. Contains Mass Quantities of Kaiju-esque Fanservice and Impressive Sprite work. A sequel is currently in the works entitled "Godzilla Replay"
Synopsis: In the far future, a human Super Soldier escapes from the Killer Space Monkey Mugal's command and attempts at destroying a capsule containing a destructive bioweapon. He fails, releasing Stalkkus, a Psycho for Hire who decides to spare the super soldier, calling him Ikibrod ("Brother" in his tongue). Refusing to associate with Stalkkus, Ikibrod goes off to find something that might have a shot at killing Stalkkus and releases an imprisoned Godzilla to do the job. Plus Mugal is still in pursuit of his two escaped bioweapons. The planet it all takes place on is revealed to be a New Eden. Humans were mostly wiped out while under the service of Mugal's forces, and Earth became Planet Daikaiju
Synopsis: A professional fanfilm that has been in production since 1970. When an explorer find himself down in a forbidden Catacomb in Spain, he becomes cursed with lycanthropy, causing him to become a Wolfman at times. At the same time, Godzilla returns to wreck havoc, which causes problems for both the main cast and the military, who is looking to eliminate them both. Often described as "The Howling and The Amazing Colossal Manmeets Godzilla."
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.Kaiju War Chronicles  by Christian Salabert, Thomas Singleton, Joshua Reynolds, Eugene Tan, Kenneth James, Kristian Zatkoff, Hayes A. Jones, Jacob Haas, Stephanie Hughes, Forrest Freund, James Webster, and Nick Anstett with new writers being still added.
Synopsis: Introducing Tohokingdom's very own K.W.C. (Kaiju War Chronicles) a huge collection of stories written by various writers. Some are connected to one another while others are their own timeline. Stories can range from just having the monsters fight each other or switching to the human's point of view and seeing the world of Godzilla through their eyes. Some stories are deep with an evil plot while others are just fun matches with just fighting. There are several epic matches some note worthy ones being the Bagan vs Everyone trilogy (matches 50, 51, 56) and Everyone vs Everyone (Match 100) and Godzilla vs Gamera (Match 14) Godzilla vs Dogora (Match 108) and many, many more. Ultraman, Gamera, King Kong, and even Zone Fighter are part of the roster''.
Synopsis: A collaboratively written epic, When Aliens Attack tells the story of Godzilla's apparent death opening a floodgate for pretty much every alien race to ever appear in major Kaiju movies to invade and fight over the Earth.
Synopsis: King and Guardian fic. They walked until the claws of their feet met the gentle caress of the oceanís waves. They turned slowly, to look back at the one who was their enemy and yet not all the same.
Synopsis: Some time after the defeat of the Xilian invasion, Tokyo faces a new threat. The offspring of the Zilla who took part in the fight, several thousand strong, converge on Japan in masses. With the vast army of monsters threatening to reproduce and overrun the world. Only the combined might of Godzilla, Minya, Gamera, and the Gotango crew can hope to stop them.
Synopsis: "One day, the Kaiju, titans of our time, vanished, and a boy was born with blazing eyes and an unnatural fury. Now, events are in motion, and they will have greater consequences than any could have foreseen." In other words, the various Kaiju vanish for some reason, and are reincarnated as humans who can transform to varying degrees to use their old powers again.
Synopsis: Remember how awesome Godzilla: The Series was? Zillah 91 sure did. Now imagine it as a series of fanfics set in Japan, free to use all the classic monsters. Godzilla? Check. Anguirus, Gigan, and Mothra? Check. It helps that each episode is very well-written and that the author has pretty obviously seen all of the source movies repeatedly, yet each story seems less like a rip-off of the original and more like fresh new perspective on the whole thing, and while the episodes ARE sequential, you can read, say, episode 8 without having read 1-5 and 7, and you can still enjoy it. Definitely a must-read.
Synopsis: A crossover fanfic involving The Little Mermaid II and Godzilla, Ariel's daughter Melody meets and befriends Godzilla, who has shrunk down to 10 feet tall after an encounter with Morgana and her henchfish. Godzilla in turn is shown the compassionate and loving side of humanity from all of Melody and Ariel's friends and family.
Pairings: Godzilla(Mamoru)/Mothra(Usagi) with a minor in Ebirah/Baragon
Synopsis: Simply, Mothra becomes Sailor Moon. In more detail Mothra, and various other Kaiju, become Sailor Scouts and Godzilla becomes Godzilla Kamen. The Sailor Scouts, and the Kaiju Sailors, deal with the Dark Kingdom, Death Busters and ChibiSpaceGodzilla, along with Godzilla's denial, and Gendo Ikari and son.