Joey Wheeler's Deck has changed numerous times throughout the series. His strategies often involve luck, which is sometimes criticized by other characters. It usually consists of Warrior-Type monsters, possibly representing his strong fighting spirit, and later support for "Red-Eyes Black Dragon".
Initially he tried filling his Deck with just powerful Monster Cards. His Deck becomes more balanced as he learns more about the game.
In the anime, Joey Dueled Duke Devlin using a Deck made from Booster Packs opened just before the Duel. Yugi objected that Joey shouldn't Duel using cards he's not used to. All the cards are from the Thousand Eyes Bible expansion of the actual card game.
Many changes are made to Joey's Deck during the Battle City tournament. With the rules changed to be closer to the OCG, Joey's Deck includes fewer high Level monsters as they must now be Tribute Summoned.
Joey's original Battle City Deck featured his "Red-Eyes Black Dragon", however he lost it in an Ante Duel, and remakes a new Deck in time for the tournament - now with "Time Wizard" as his rare card. Additionally, he wins more rare cards from the duels he wins in the preliminaries.
The number of tough Warriors and Beast-Warrior-Type monsters decreases and he includes a few cartoon-like warriors, while many more luck based cards are added, a trait that leads Esper Roba to dub it a Gamble Deck.
Although Yugi manages to win back Joey's "Red-Eyes", Joey refuses to take it back and says he'll earn it when he becomes a better Duelist (in the English dub, he lends it to Yugi to help defeat Marik). In later arcs of the anime, he is shown to have it again, so it is assumed he defeated Yugi in the Duel following the tournament. In the manga Jonouchi does not use it again, except in Millennium World, where he wouldn't necessarily need the actual card, but it is eventually confirmed that he has re-obtained it when he shows the card to Aigami in Yu-Gi-Oh! The Dark Side of Dimensions.
During the tournament, Joey is possessed by Marik Ishtar and is forced to Duel Yugi with additions to his Deck made by the Rare Hunters. He runs a Burn Deck. Marik adds a number of Magic Cards to his Deck, which allow him to directly destroy monsters and inflict damage, although such cards were outlawed in the Battle City tournament.
After losing to Yami Marik, Joey falls into a coma, in which he dreams about the tournament he entered in episode 2, using his original Deck based on Warrior-Type monsters. (In the dub, he dreams that he is participating in a different tournament.)
In Noah Kaiba's virtual world, Joey was made to construct a Deck to use in this world. He made one close to his Battle City Deck, but also included a number of "Harpie" cards as a tribute to Mai Valentine.
Jonouchi's Deck is similar to his Battle City Deck, but has advanced slightly in each of his play-styles. He retains his rare and luck-based cards, having acquired more of both, and continues to occasionally use Fusion Monsters. The most notable addition to his Deck is the "Time Machine" card that he took from Bandit Keith after the Duelist Kingdom arc.
Joey Wheeler is a Level 3 opponent in World Championship Tournament 2004. In order to unlock him, the player must defeat all of the Level 2 Duelists at least five times and have a "Jinzo" in their Trunk, but not in their Deck. If they can amass at least ten wins and maintain at least a 50% win ratio against Joey, the latter stipulation no longer applies.
Fitting his aggressive personality in the anime, Joey's Deck is full of high-ATK monsters, primarily Warriors and Beast-Warriors. Many of his Level 4 monsters have 2000 ATK or more, but suffer from various restrictions, such as changing to Defense Position after the Battle Phase or losing ATK for every monster destroyed. He also has some dangerous Effect Monsters, such as "Jinzo" and "Time Wizard", and he almost always activates the latter's effect successfully, making it difficult to keep monsters on the field.
He has generic Spells and only a few Traps, which mostly focus on strengthening his own monsters or getting rid of his opponent's monsters to give him a clear shot at their Life Points. If he gets the chance, he'll also use "Polymerization" to bring out one of three deadly Fusion Monsters: the 1700-ATK, potentially-Direct Attacking "Alligator's Sword Dragon", the 2400-ATK "Thousand Dragon", or his strongest monster, the 3200-ATK "Black Skull Dragon".
On the other hand, Joey's Deck has no Spell or Trap negation apart from Jinzo, and very little defense against monster Summons (other than his "Ring of Destruction" cards). He also tends to Summon "Time Wizard" in Attack Position to make use of its effect immediately, which leaves him vulnerable to taking a large amount of Battle Damage from a powerful monster.