In Ascending Order of Date Published

as a Main Pairing

Birds of Paradise by yllimilly - LiveJournal - No Rating (Wayback Machine Backup Link)
     No Summary. Response to Prompt: "Siegfried von Schroeder X Malik Ishtar; Flowers"

Desert Rose by RosalindHawkins - AO3 - Mature
     The classic love story of a German and an Egyptian. Okay, not really "classic," but a love story nonetheless.

Of Kings and Dragonslayers by NyanbinaryRose - AO3 - Teen
     Malik was expecting a lot of things to happen at this party. He did not expect this.

lavender by UnfriendlyAmazon - Tumblr - Teen (Wayback Machine Backup Link)
     He brings you lavender, no matter what you do to him. An exploration of darkness and devotion for Malik Ishtar.

Defy Expectation by NyanbinaryRose - AO3 - Explicit
     Malik's not a fan of holidays, but after his first Valentine's Day with Siegfried, he may be willing to make an exception.

Pure Fantasy by NyanbinaryRose - AO3 - Explicit
     Malik asks Siegfried about his desires and gets a very honest reply.

Better to Serve the Devil by NyanbinaryRose - AO3 - Explicit
     In another time they could have been close friends. A cute couple, even. But instead, on the eve of Battle City, Siegfried finds himself in a deal with the Devil. The Devil calls himself Malik Ishtar.

[Alternatively, "What if Siegfried became a hacker for the Rare Hunters during Battle City?", or more broadly, "Two antagonists meet and make each other much, much worse"]

          Part 1 of The Devil and His Devotee (Incomplete Series)

Partition by NyanbinaryRose - AO3 - Explicit
     Siegfried gives Malik a quick blowjob on the way home.

aberrant by UnfriendlyAmazon - Tumblr - No Rating (Wayback Machine Backup Link)
     Zigfried draws Malik's portrait. It goes about as well as you'd expect.

as a Secondary Pairing

Trial By Fire by NyanbinaryRose - AO3 - Rated Teen
     Everything seems peaceful since Atem left, but when trouble stirs in Hawaii, it's up to Yugi, his friends, and even some former enemies, to save the world from the war raging between two sister goddesses: Pele-Honua-Mea, and Namaka-o-Kaha'i.

as Part of a Multiship

Masquerade! by just_a_ghost_69 - AO3 - Explicit
     When the masks come off, everyone just wants to have a good time.

          Malik x Siegfried x Otogi (Duke) x Kaiba

A Notable Exception by NyanbinaryRose - AO3 - Explicit
     Siegfried and Malik have spent the last decade living together and loving together. They're as happy of a couple as can be- with one notable exception. Everyone has fantasies after all, and much to Malik's chagrin, only Seto Kaiba can make them reality.

          Malik x Siegfried x Kaiba