But I've been watching Lois and Clark lately, and it occurs to me that Yu-Gi-Oh takes the great Superman story and character archetypes and runs with them.
The hero with a loving family, albeit not his direct birth parents, comes from a tender, loving household. Then one day, he discovers he is very different from everyone else.
* Clark Kent is the persona created by Martha and Jonathan Kent for the little boy they found in a spaceship abandoned in a field near their home in Smallville, Kansas. They raised him as their own, hardly aware that the boy --though a human, for all intents and purposes-- possessed super powers thanks to the light of the yellow sun.
* Yuugi Mutou is a young boy living with his grandfather (and his mother; his father is said to be alive, but he's constantly "away on business." In any case, it's Sugoroku who does most of the raising, and has had the most influence on Yuugi's life). He doesn't make himself too well known and out there; he seems to know that he's different somehow, what with his love of games. Then, one day, he manages to solve the elusive Millennium Puzzle, and he unlocks another side to himself...
At first, he has to conceal his other self. He doesn't know whether it will harm others or help them, so he disguises it at every opportunity. Eventually, he grows into his "other self", but it still causes problems for him.
* Clark adopts the Superman persona only after he arrives in Metropolis. Lois Lane is actually the one that names him. He starts to help people, stop crime, etc., but he keeps his "other identity" a secret. Slowly, but surely, his presence angers enemies all around him. Meanwhile, Clark desires to live a 'normal' life while still helping as much as he can. He gets the beginnings of an identity crisis as people see Superman and Clark Kent as two different people-- including Clark's love interest, Lois.
* Yuugi slowly becomes aware of his "other half," Yami no Yuugi, otherwise known as the (formerly) Nameless Pharaoh. At first, YnY just takes control of Yuugi whenever he can/feels like it, and actively takes revenge on those that wrong Yuugi and his friends. He makes enemies of all of them, though few ever survive to let their anger stew for very long. When Yuugi finally does become aware of his other half, he still doesn't know too much or trust him. At Duelist Kingdom, he even stops YnY from attacking Kaiba's monster, thereby allowing Kaiba to win the duel (and not 'commit suicide').
There are also striking character similarities:
Yuugi <--> Clark (shy, hardworking, determined, values friends and family very much)
Yami no Yuugi <--> Superman (mysterious, elusive, powerful, a bit arrogant)
Anzu <--> Lois Lane (independent, headstrong, too curious for her own good. Falls for the hero, but not who the hero "really is"-- at first)
Jounouchi <--> Jimmy Olsen (funny, but intelligent, dedicated, but often gets into trouble)
Sugoroku <--> Jonathan Kent/Perry White (a father and mentor figure. Someone the hero would save under any circumstance)
Seto Kaiba <--> Lex Luthor (rich, arrogant, egotistical, can't stand to be beaten. Has also 'come back from the dead')
Yami no Bakura <--> Tempus (unhappy with the way things turn[ed] out, sneaky, though often thought to be insane)
Mai <--> Mayson Drake (bold, independent, sexy blonde-- though she's never shown an interest in Yuugi, as Mayson did for Clark. She DOES get Anzu riled up, though)
Gebeluk <--> Nigel St. John (a servant/worker of the hero's rival/worst enemy, he's sneaky, evil, and dies by his own foolishness)
I can't think of any similarities for Isis (maybe that woman that appeared to tell Superman/Kal'El that he had a 'greater destiny'), Malik (said woman's nutty companion?), Ryou Bakura, Honda, Shizuka, Otogi, and a few others... maybe you can? Remember I'm drawing these similarities from the L&C TV series, not the Superman comics or anything. Hence the decided lack of Supergirl or anything like that.
But what do you think? Creepy, no?