Atem, while more flawed than Yugi, also fit this trope, especially in later episodes. He has proven to be a kind, heroic, and caring soul who fights for what is right. He will do anything to save the people he cares about.
Téa also qualifies for Nice Girl as she is always there for her friends, is extremely supportive, and has the kindest heart.
Jaden Yuki in Yu-Gi-Oh! GX. In the earlier episodes, Jaden is naive but overall a very pleasant person. He's optimistic, kind-hearted, helpful, and caring. In one episode, he accepts a challenge from an Obelisk snob with a wager, where the winner gets to be Alexis's fiancée — despite the fact that he honestly doesn't know what a fiancée is. Somewhat deconstructed in the later seasons as the escalating risks and losing his friends take a toll on him. This culiminates in revealing he has a Superpowered Evil Side that causes him no end of problems later, and once he recovers from it, not everyone is pleased with the fact that he seems to be much more serious from the experience. Thankfully Jaden does seem to return to his nicer traits by the end of the show.
Alexis Rhodes is one of the few nicer Obelisk Blue students in Duel Academy, as she doesn't treat Slifer Reds or Ra Yellows as lesser than her the way most Obelisk Blues do.
On that note, Jesse is probably a straighter example than Jaden. He actually is a genuine nice guy, with no Superpowered Evil Side trying to say, take over, and selfless enough to pull a Heroic Sacrifice. Twice. And that for people he barely knows. Nice Guy ahoy.
Jim "Crocodile" Cook also counts as this. Jim is just a friendly guy at Duel Academy that loves dueling and discovering fossils. When the cast gets into trouble he's there every time to lend a hand to stop Viper, help Duel Academy in the different dimension, and search for Jesse. Once the Supreme King has Jaden trapped within, Jim goes to extreme lengths and puts his life at risk just to save his friend. The guy is a saint.
Yusei from Yu-Gi-Oh! 5Ds is also a Nice Guy. Appearances and backstory aside, he is extremely heroic, friendly, kind-hearted, mature, caring, and selfless.
Yuma Tsukumo of Zexal, like the other protagonists before him will always choose his friends over himself. His kindness and sympathy for everyone is quite genuine which makes him a very admirable character.
Yuya Sakaki in Yu Gi Oh ARCV continues this trope. He is a fun-loving, cheerful, protective, and caring kid who only wants to make the world smile as an "Entertainment Duelist".
Yuga in SEVENS is a very benign individual. Not only does he not care about being "Duel King" and is happy to have his friend Luke take on that title, he also just wants to create a new form of dueling that everyone can enjoy. After seeing Gakuto being legitimately stressed from handling so much paperwork, reprograms Kaizo into handing it to lessen the burden.
