Jaden Yuki's Deck has gone through a great amount of changes both the anime and manga versions of Yu-Gi-Oh! GX. It is most famous for his "Elemental HERO" monsters, which fuse in various combination to create more powerful monsters.
His manga incarnation still uses "Elemental HEROES", though he does not generally use the same ones that his anime counterpart utilizes. He later begins using the "Masked HERO" series of cards in place of them.
So far, he has been featured in more Duels than any other character in the franchise.
During the first year, Jaden plays an Elemental HERO Deck, composed of Spell and Trap Cards that support them, as well as his spirit partner "Winged Kuriboh". His deck largely supports Fusion Summoning stronger Elemental HEROES, often using a colorful array of Spell Cards, which have additional effects besides the aforementioned effect, allowing great flexibility in strategies. All Elemental HEROES fuse in some combination, granting Jaden a myriad of different effects to take advantage of. Some of his spell and monster card combinations serve as back-up strategies. His strategies are always full of surprises and he always draws the right card when needed.
Jaden continues to use his Neos Deck in Season 3, debuting more advanced Neo-Spacian tactics. This includes fusions involving "Elemental HERO Neos" and two, rather than one Neo-Spacian monsters as well as usage of the Chrysalis monsters. After being freed from the influence of The Supreme King, Jaden keeps the "Super Polymerization" card, which proved to be one of the keys of ending his continued conflict with Yubel.
In his third year while possessed by The Supreme King, Jaden plays an Evil HERO Deck, which consists of vile incarnations of his regular Elemental HERO Fusions. As opposed to his flexible strategies that he normally uses, this Deck consists of a much more straightforward approach that simply overpowers his opponents with the deadly effects of certain Evil HEROES, as his trademark card, "Dark Fusion", protects the SummonedMonsters from being targeted by his opponent's effects.
In Season 4, Jaden begins using a variety of cards he used from the previous seasons, especially from Season 1. The most noticeably change in his Deck is the new usage of "Super Polymerization" and "Yubel" herself. He's able to use the former to fuse the latter with "Elemental HERO Neos" to create "Neos Wiseman".
In the manga, Jaden uses an Elemental HERO Deck, different from that of his anime counterpart. The Deck once belonged to Koyo Hibiki, but Jaden had modified it throughout the years. Though he later switches to "Masked HEROES" as he felt that he dishonored Koyo while Dueling Reggie MacKenzie, Jaden uses this Deck once more against Tragoedia, wanting to symbolically stand with Koyo to defeat the monster that put him into a coma.
In Yu-Gi-Oh! GX Tag Force, Jaden initially uses a Deck similiar to that of his anime counterpart, though he has less Fusion Monsters. He later uses more powerful Decks, that include the stronger Fusions.