Yako Tenma's complete 180 during his duel with Kaiba where after spending a few chapters getting beaten with little to no trouble he manages to effortlessly turn things around and completely curbstomb him. Even better? He's the only Big Bad in manga or anime canon to defeat Kaiba without cheating.
It's also worth noting that, during the duel between Kaiba and Jonouchi/Joey in the Battle City arc, Kaiba was understandably pissed off when Joey managed to summon a Blue Eyes White Dragon on his side of the field. So imagine how Kaiba must have felt when Yako summoned all three of Kaiba's Blue Eyes on his side of the field... and then treated them as sacrifices as if they were nothing.
Yako's twin brother Gekko's duel with Ted Banias. At first, Gekko appears to be using a half-baked strategy built around building up his hand with Graceful Charity and playing the defensive. He begins to lose so badly that Banias and Keith begin taunting him with the implication that he's losing on purpose, just so that he'll allow his brother to continue on with his plans. But then, just when Gekko's about to lose, he summons five of his equip-spell cards from the graveyard, and then it's revealed that he was planning this all throughout the entire duel, using Graceful Charity as means of sending his equip spells to the graveyard only to bring them back later. He then activates their abilities, allowing them to cut through Banias's monster and move in on his life points, granting Gekko victory. Pegasus clearly didn't call Gekko a perfect duelist for nothing.
Yako gets another one when Yugi calls Ra from the graveyard, and you think that he's either going to go One-Turn-Kill or God Phoenix (probably the latter), just as Yami Marik used to do so...and then Yako negates the Summon. One of the previous Big Bad's best moves used by the protagonist made wasted just like that.
And finally, the final Duel against Yako is a massive one with heaps of tributes to Yugi's duels with Kaiba and Marik thrown in. And how is the Wicked Avatar, always the strongest monster on the field by one point, finally taken out? Yugi Summons Obelisk, uses its effect to boost itself to infinity, thereby making equal to Avatar's, and THEN upping it's divine rank to avoid the utter failure he had when he used that effect against Ra, resulting in Obelisk gaining a completely awesome new form, and both monsters destroying each other.
Yako: He only has 98 life points left...but he might as well have 98,000.