The YGO Shippedia

Bandit Keith, Yami Yugi and Yugi Moto

So named because while Yugi was trying to rescue Yami Yugi from Keith (possessed by Malik at the time) a fire was starting in which Yugi was severely burnt.

Hiroto Honda and Katsuya Jonouchi

Bandit Keith and Dinosaur Ryuzaki

So named because Bandit Keith acts brutally towards others and Dinosaur uses brutal dinosaur cards in his duels.

Yami Malik and Malik Ishtar

So named because Malik has "bronze" coloured skin; the same is true for his "darker personality," who technically has no body of his own.

from seventh-star

Mai Kujaku and Dinosaur Ryuzaki

So named because Mai gave Ryuuzaki a bribe to due Jounouchi.

Shaadi and Cyndia

So named because both characters are viewed as being deceased, therefore they could not draw breath.

Mokuba Kaiba and Anzu Mazaki

So named because during episode 72, while Anzu and Mokuba were kidnapped and held in a warehouse, Anzu formed the idea of stacking up some cardboard boxes and climbing the pile to reach a window. Mokuba manages to reach the window before the boxes collapse, sending Anzu (and the Ghouls who kidnapped them and were trying to stop them from escaping) tumbling down. As he runs away, Mokuba promises to send help for Anzu.

Thief King Bakura and Yugi Moto

So named because both characters are bound to their destinies.

Yami Malik and Ryuuji Otogi

So named because some fans like to joke about them having an attraction to bondage.

Seto Kaiba and Kisara

So named because Seto and Kisara both have blue eyes and connections to the Blue-Eyes White Dragon.

from seventh-star

Yami Malik and Gozaburo Kaiba

So named because both characters caused much suffering to others and were probably the cause of some blood spills.

Pharaoh Atem(u) and Yugi Moto

So named because both characters could be seen as having a blind devotion to each other.

Priest Mahaado and Shizuka Kawai

So named because both character see themselves as being blessed in some way; Shizuka because she has a brother like Jounouchi and Priest Mahaado because he can serve the pharaoh.

Katsuya Jonouchi and Shogo

So named because when Jounouchi rescued the Red Eyes Black Dragon for Shogo he was regarded blankly by the child.

from seventh-star

Possessed Katsuya Jonouchi and Anzu Mazaki

So named because these characters could be seen as the blame for why Yugi was lured into one of Malik's traps.

Pandora and Yugi Moto

So named because Pandora used blades against Yugi during their duel.

Yuma Tsukumo, Astral and Kotori Mizuki

Yuuma believes in his Kattobingu to succeed. Kotori and Astral mutually believes in Yuuma and his willpower of Kattobingu as well. Kotori believed in Yuuma he’d come to rescue his friends when they were captured.