During Duelist Kingdom, Yugi uses a deck comprised of mostly low-LevelEARTH and DARKMonsters and some Equip Spell Cards to increase their abilities. The deck also originally had the Exodia 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.
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 Spell Cards that are designed to destroy or negate the effects of his opponent's Spell Cards and Trap Cards. The rarest card in his Deck (aside from the previously lost Exodia) is "Dark Magician", of which he has only one. (Though during Battle City when challenged by Arkana the winner of that duel would obtain the loser's Dark Magician. Although Yugi won, it's unknown whether he actually took Arkana's Dark Magician but if he did, he never used it. It is unlikely that Yugi would use Arkana's Dark Magician card as he determines during the duel that it has been tampered with, having its edges trimmed.)
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.