Yugi plays a Strategy Deck, containing various flexible strategies for any situation, however, two Types that can be seen consistently throughout Yugi's Decks are the Fiend-Type and the Spellcaster-Type, possibly to reflect Yami Yugi's mystical and somewhat dark nature.
Yugi originally uses the Deck built by his grandfather, Solomon Muto in a rematch against Seto Kaiba. Solomon had previously added his prized card, "Blue-Eyes White Dragon" into the Deck for the Duel, but it was subsequently destroyed by Kaiba upon Solomon's defeat.
Yugi inherited the Deck and subsequently built his own, containing many of the staple cards collected by Solomon. Yugi used this Deck against Pegasus, and brought it to compete in Duelist Kingdom, however the Deck was radically altered again once the pieces of Exodia were lost by Weevil Underwood.
In accordance with Battle City's ante rules, whenever Yugi won a duel, he would gain the rarest card his opponent's deck along with the Locator Card needed to participate in the finals. After defeating the Rare Hunter, Seeker, he got back the "Red-Eyes Black Dragon" that was taken from Joey after he lost it in a previous duel and was prepared to give it back to him, but Joey let him keep it as a sign of their friendship, which proved invaluable when they were forced to duel each-other by Marik. Yugi also gains ownership of Arkana's unique Dark Magician after beating him, but never used it in a Duel, presumably because it was illegally trimmed. It wasn't until he defeated Marik's human puppet, Strings that he obtained his first Egyptian God Card, "Slifer the Sky Dragon", which he didn't use until the Battle City finals. However, he wasn't seen taking anything from Lumis, Umbra or the other two Rare Hunters he defeated in tag-team duels with Seto Kaiba, likely because he was more focused on saving his friends.
Yugi's Virtual World Deck is largely similar to his Battle City Deck, though he did not have the luxury of his God Cards. He also included several (retrained versions of) cards he had formerly used in Duelist Kingdom, but not in Battle City. He also introduces new support for his Duelist Kingdom themes, such as "The Rock Spirit" (EARTH monsters) and "Sangan" (low ATK). For his Duel with Noah Kaiba, Yugi would shuffle his Deck together with the remainder of Seto's own.
Yugi plays a Kuriboh/Spellcaster/Timaeus Deck during the Waking the Dragons arc, focusing on Summoning the 5 Kuriboh Brothers through "Five Star Twilight" and combining them to form "Kuribabylon" and raising its ATK through "Pump Up" and "The Seal of Orichalcos" (the latter when he was under its influence). He also makes use of his "The Eye of Timaeus" card he received in order to defeat Dartz, by fusing it with his Magicians in order to Summon powerful Fusions. He supports his strategy by using "Excalibur" or "Altar of Restoration". Because of Yami's loss to Rafael, Yugi's soul was taken and thus he played no part in the Duels for the rest of the season, save a Duel against Yami that acted as a test of the latter's character. Cards used by Yami after this point are listed at Yami Yugi's Decks, as Yugi had no part in any further alterations to the Deck.
In the movie, Yugi's Deck adds more support for his "Dark Magicians" as well as a higher amount of resources devoted to Summoning the God cards. Only the cards used by Yugi in his Duel were shown in the film, but the full Decklist (totaling out to exactly forty cards) was given in the novelization of the film.
In Yu-Gi-Oh! GX, Yugi's Deck featured cards that he had previously used in a variety of arcs, including some not seen in a while. The Duel between him and Jaden Yuki is known to have taken place sometime after a second version of Battle City.
In Yu-Gi-Oh! The Dark Side of Dimensions, Yugi runs a hybrid Deck mixing cards of his own and cards he inherited from Atem. He uses a number of retrained versions of iconic monsters of the both, including brand-new Spellcaster-Type support cards for Atem's "Dark Magician" and "Dark Magician Girl". He also has lots of tactics involving Continuous Trap Cards, such as a number of Trap Monsters and the "Dimension" Trap Cards he calls the "Dimension Trap Pyramid".