AOA: Explosive Relations: By Alexandra Nigro.
In the AOA, Gambit joins up with Magneto, Rogue and the X-Men for the first time.
Mystery Dark Elf 3000: By Anya.
Magneto and three characters from another fandom are trapped on the Satellite of Love and forced to read bad fanfic. Humor.
Daughter of the Sun: By Dawn Bobby.
An AOA tale in which Sabretooth and Magneto come into conflict over a woman Creed trusts and Erik doesn't.
Choices: By Dimira Marka.
A non-canon tale of Joseph's origin in which he is Magneto.
A Pound of Flesh: By Indigo.
Sequel to "Crimes of the Heart." Joseph is a character in this story. This is unfinished, and never will be finished to the best of my understanding, but I am still really interested in recovering this one.
Marvel-X: X-Men: By Jason Kenney.
An on-going series in issue format. The story arc "The End of the World" features both Magneto and Joseph, being an alternate take on the Magneto War.
Memories: By Kerrin Watter.
Logan meets an old friend on the road, a woman on a quest to find "Joseph" and help him restore his memories before it's too late... (Classified as a Secondary Character Story because, even though the plot is largely about finding Joseph, he himself barely appears in it.) I believe Ms. Watter has probably removed this from circulation for being too old.
Enigma: By Kerrin Watter.
A young mutant woman gets sucked into the X-Men's world when she attempts to save Gambit and ends up a captive with him. Magneto is leader of the X-Men in this story. This was a pretty egregious Mary Sue, so I'm pretty sure the author removed it deliberately.
Marvel-X: X-Men: By Kyle Trainer.
An on-going series in issue format. The story arc "The End of the World" features both Magneto and Joseph, being an alternate take on the Magneto War.
The Dragon and the Phoenix: By Lady Phoenix.
In a world where Phoenix became a member of the Hellfire Club by choice rather than coercion, the introduction of a mutant sorceress named Tai causes disruption to the Club. Magneto is one of the Lords Cardinal of the Hellfire Club in this story.
Always, His Woman: By Linda McWray.
Hank gives Rogue a device that allows her to touch, and her choice is Remy, not Joseph. But will either Remy or Joseph fully believe that? This story contains some scenes of sex between Rogue and Remy. It's disclaimered "violence" as well, but in my opinion the "violence" isn't all that serious for a story about superheroes.
A Lack of Myself: By Northlight.
Joseph thought the worst possible thing was to know he had been the evil Magneto... but now that that has been called into question, he finds that not knowing is worse...
Games People Play: By Pamela Thalner.
Joseph falls for a woman named Lee Holland, whom Remy has some history with.
Marvel Tangent: Magneto: By Rahne Sinclair.
The Marvel Tangent universe is a spinoff universe which purports to be completely different, similar to DC's Tangent line, so despite the fact that this story could well be about the MU's Magneto, I've labeled it Alternate Magneto. Magneto has retreated from the world, to Antarctica, with only a young girl to keep him company. But the world doesn't wish to let him go...
Blinking Into Existence: By Reuben "Supereub" Macapinlac.
The return of Blink. Cast consists largely of Joseph, Wolverine and the Gen-X crew.
The Clone Report: By The Uncanny X-Girls.
Five (basically) normal women talk Sinister into letting them beta-test clones of Magneto, Sabertooth, Beast, Dark Beast and others. Parody.
X-Men: Decimation: By Wolvie.
Charles Xavier's death prompts a terrible chain of reactions.