Yugi Muto's Decks

Duelist Kingdom
During Duelist Kingdom, Yugi uses a Deck that originally belonged to his grandfather. It is comprised of mostly low-Level EARTH and DARK Monsters and some Equip Magic Cards to increase their abilities. The Deck also originally had all five pieces of Exodia the Forbidden One cards in it, which he used in the first episode to defeat Kaiba, but on the ship to the Duelist Kingdom, Weevil Underwood threw them overboard, and even though Joey Wheeler attempted to save them, only two of the five pieces were ever recovered, which were the head and the right arm.

Special Deck
In episode 13, Yugi combines some of Joey's, Téa's and Tristan's cards into his Deck against Bakura/Yami Bakura.

Battle City
During the Battle City arc, he keeps the theme of having EARTH and DARK monsters with dangerous effects. His Magnet Warriors become a major part of his Deck, as does his "Dark Magician Girl". His Deck from Battle City onward focuses more not only on his "Dark Magician", but also on his manipulation of his Magic Cards that are designed to destroy or negate the effects of his opponent's Magic and Trap Cards. The rarest card in his Deck (aside from the previously lost Exodia) is "Dark Magician."

As the series progresses he begins to add more and more support for his "Dark Magicians", such as "Dark Magic Curtain", "Magical Dimension", and "Sage's Stone".

Virtual World
His 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 cards he had formerly used in Duelist Kingdom, but not in Battle City.

Waking the Dragons
Yugi's Deck now featured more support for Kuriboh and Dark Magicians and now had "The Eye of Timaeus". 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.

Grand Championship
His Deck continued to feature additional support for his Dark Magicians and also began to add more support cards for his Knights. In addition, most of his Kuriboh support cards made no appearance.

See also: Rick, whose Deck Yugi used against a Duel Robot.

Dawn of the Duel
During the Dawn of the Duel arc, Yugi uses a Deck based around cards with a Toy theme and LV monsters such as "Silent Swordsman" and "Silent Magician". This Deck represents the strength Yugi has without the help of Yami Yugi as well as his playful side. Notably, Yugi's Deck does not feature Dark Magician during this arc, though Yami's did.

Pyramid of Light
In the movie, Yugi's Deck adds more support for 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.

GX
In Yu-Gi-Oh! GX, Yugi's Deck featured cards that he had previously used in a variety of arcs, including some not seen since Duelist Kingdom. The Duel between he and Jaden Yuki is known to have taken place sometime after Battle City.

Yugi's Deck went on tour at Duel Academy at one point, where it was stolen by Dimitri. He used it in two Duels, and it focused on retrained Chaos versions of Yugi's Ritual Chaos monsters.

In episodes 168 and 179, a replica of Yugi's Deck is shown, which was to be given to the student who did the best in the graduation Duels.

R
In Yu-Gi-Oh! R, Yugi uses a Toy Deck, centered around Yugi's childish side, using cards such as "Toy Magician" and "Toy Box". Similar to the Dawn of the Duel arc, Yugi and Yami utilize separate Decks.