I’m sorry
Many questions have deliberately been left open in Nintendo’s many franchises. Why do Mario and his enemies get together for friendly games of tennis? Are there normal animals in the Pokémon world? And what’s going on with the Kong family tree, anyway?
But one subject on which Nintendo is more evasive than any other is the question of parentage. People just seem to come into being in these worlds fully formed, like Athena springing from the head of Zeus. But some parents do, canonically exist in the worlds of Mario, Pokémon, and Zelda. And some of these parents have biological children.
Which means, canonically, that a number of Nintendo characters have, well,

How many, though? As a purely scientific endeavor, I set out to learn the dark truth. But before I get to the list, a note on which characters I’m excluding:
First, Mario and his friends—Wario, Luigi, and so on. These characters are shown to have been delivered by stork in the Yoshi’s Island series, making it unclear as to how they were conceived. Maybe parents just wish real hard and a bird reads their minds and horks up a baby.
Second, characters who don’t actually appear in games—people like Ness’s dad, who does save your progress but whom we never actually see.
Third, all Pokémon. While breeding is a central mechanic in the series, Nintendo has been evasive on how this actually works, landing on “eggs just appear when Pokémon hang out” and “they aren’t even really eggs at all,” allowing us to dispense with the problem of the Skitty and the Wailord.
And finally, Goompapa from the Paper Mario games, because I’m pretty sure Goombas are a kind of mushroom, and I think they just do something with spores. I didn’t see Oblivion, so I’m not totally sure.
Bowser

I want to be clear here—as of 2018, Bowser has canonically nut only once, resulting in the birth of his son Bowser Jr. The mother of this child is unknown, but is widely speculated to be Princess Peach based on Jr.’s obsession with her in Super Mario Sunshine. However, when asked who the younger Bowser’s mother was, Shigeru Miyamoto suggested it was none other than himself.
What about the Koopalings? While they were once described as Bowser’s children, they are now simply a gang of rowdy kids he adopted ala Max in The Lost Boys.
James McCloud

No bones about this one—he’s Star Fox’s dad, a hero who died tragically fighting in the first war against Venom. And in his newer depictions, he’s got a definite Master Miller from Metal Gear Solid vibe going on with those sunglasses. But who was Fox’s mom? According to the 1993 comic, her name was Vixy Reinard. In this version of the story, Andross had become infatuated with her and planned to get James out of the picture with a car bomb, as you do. Tragically, Vixy used the car that day, making Andross responsible for the deaths of both of Fox’s parents.
That said, the comic isn’t canon, so the identity of Fox’s mother is still an open question in the games. Maybe she wasn’t a fox at all. Maybe she was actually a rabbit. It worked in Zootopia.
Pretty Much Everyone in Fire Emblem Awakening and Fates

Depending on how you play, pretty much every character in these games has the potential to have biological children. However, I would be remiss not to mention that these children arrive from the future in Awakening, meaning that in the present timeline of the game, their father may not necessarily have nut. Let’s not get into how Fates needed to duplicate this popular mechanic without relying on time travel, and so used a time-accelerated pocket dimension to achieve the same effect—meaning that the parents were separated from their spawn until at least their teenage years.
The only character, then, who can be said to have done it in Awakening is Chrom, who marries one of a number of eligible bachelorettes, including the player. How many people got bushwhacked into marrying him and birthing his time-traveling daughter when they were saving themselves for Gangrel? Not okay.
Norman

The first and thus far only present player character father in the Pokémon series, Norman is a gym leader whom the player must best in order to move on in their quest to become a champion. He may live for Pokémon, but he took at least some time away from his obsession to impregnate Brendan or May’s unnamed mother.
Cranky Kong

The Kong family tree is kind of contentious, but I’m working on the assumption that Cranky Kong is Donkey Kong’s grandfather—and he’s the DK of the original series, which makes DK Jr. his son. So, at some point, Cranky Kong got it on with the dearly-departed Wrinkly and we were introduced to the now-vanished Jr.
You might want to extend this chain of thought to assume that DK Jr. should also be included here. However, as I noted above, in the present-day tie-wearing Donkey Kong’s appearance as a baby in the Yoshi’s Island series, he is clearly delivered to his parents via stork. We simply don’t know the mechanics of bird-based baby delivery systems, and so we can’t be certain about DK Jr.
Slippy Toad

There’s a lot we don’t know about the Star Fox universe, but the amphibiously aware reader might argue that anthropomorphic frogs reproduce via external fertilization. To that, I say two things. One: it still counts. Two: hasn’t Slippy suffered enough? Let him have this.
Talon

What we know about Talon: he is the owner of the Lon Lon Ranch. His wife never appears in the Zelda series. He is based on Mario. He has done it at least once.
Bonus: Dr. Eggman

This one’s a little complicated because of conflicting backstories for Eggman Nega, a character who appears in Sonic Rush and the Sonic Rivals games. In the former, he is established as a version of Eggman from the same alternate universe as Blaze the Cat. However, in the Rivals series he is Eggman’s time traveling descendant. Which to believe?
Well, in 2012 Takashi Iizuka—a prominent member of Sonic Team—gave Word of God that Eggman Nega and Silver are from the future of Sonic’s world, whereas Blaze is from another dimension. Ergo, Eggman joins the illustrious ranks of his comrades at Nintendo—albeit one whose time is perpetually yet to come.
Joe
December 14, 2018Eggman isn’t a Nintendo character. Sonic is owned by Sega.
The Big Man
December 21, 2018its a bonus kid
let the man have his moment
Smooth Jazz McDonald
December 15, 2018actually brock’s dad appears in the pokemon anime and that dude did a lot of nutting. there’s a whole squadron of his children
varewulf
December 16, 2018There’s also Captain Olimar from Pikmin who has a wife, daughter, and son that show up in Pikmin 2 via email messages from his home planet.
Matthew
December 16, 2018When Koga becomes a member of the Elite Four his daughter takes over his gym.
John Piland (Kurapikachu404)
December 20, 2018King Daltus, King Daphnes, King Rhoam, King Dorephan, and Kass have all nutted
Kenneth
December 20, 2018Lucina and Chrom are Marths decendents, also he marries Caeda at the end of Myteries of the emblem
ruby
December 20, 2018oot link also has nutted because tp link is his descendant.