A joke using this: two new parents stare at their newborn in disbelief, wondering how one child can have so many different attributes (sometimes they're listed: blond hair, black skin, small nose, huge ears...). Then they recall having participated in an orgy some nine months back. The baby starts crying, at which point the mother expresses relief that at least he isn't barking.
In Isaac Asimov's novel The Gods Themselves, the alien Soft Ones have three sexes, all of which are required for reproduction. The one that actually gets pregnant is referred to throughout using male pronouns.
In the Gor series, the alien Kurii have three (or four) sexes, or genders. They basically work out to be male, female, a "blood nurser" which the females lay their offspring in and then the babies eat their way out of, and a fourth sex which is essentially a male with low testosterone, which is shunned by the community, but in certain circumstances becomes a breeding male; hence they're not sure whether to consider it a separate sex or not.
There is a story by Stanislaw Lem about aliens who, among other things, have five sexes.
Merry Gentry: Merry eventually gets pregnant with twins, and the twins have three fathers each.
A gag to this effect appears in the Rod Albright Alien Adventures series, when one alien mentions that normal honorifics and pronouns don't apply well to "him", because he comes from a species that requires five genders just to produce an egg, and three more to hatch it. Perhaps fortunately, he doesn't go into detail on this absurd arrangement.
The Player Of Games by Iain M. Banks: The Empire of Azad is ruled by a humanoids with three genders. Male, female and apex. An apex has a reversible set of equipment and carries the fertilized embryo from male to female. All three genders contribute genes, but the knowledge that females are more than passive child bearers is suppressed: the apices are very much on top and exercise crushing sexual discrimination against both other genders.
The Yeerks of Animorphs are sluglike aliens whose reproduction apparently involves three of them fusing into a single mass, from which larvae spawn.
Mr. Fusspot, the canine bank Chairman from Making Money, is metaphorically described as "the son of many fathers". His spoonhound mother got loose while in heat, and her owners never learned what male dogs she'd encountered before coming home pregnant.
In Slaughterhouse Five by Kurt Vonnegut, the Tralfamadoreans reproduce with three genders, and further claim that humanity actually requires more than that to reproduce (although only two need to be physically performing the deed in three dimensions; the others are involved in an unspecified extradimensional way).
In the Ringworld series the Puppeteers have three sexes. The first two are basically male and female, and they parasitically lay eggs in the third. The third gender is implied to be nonsentient.
In The Discovery Of Heaven by Harry Mulisch (also made into a film), the child who brings the Laws of God back to heaven has one mother and two fathers. Ada, the mother, has sex with both men on the same night.
The Newcomers in Alien Nation. Tenctonese have three sexes — male, female, and binnaum — all three of which are necessary to have a child. Because binnaums are relatively rare, they traditionally live monastic lives, only having sex when they are asked to help fertilize an egg for a male/female couple.
One episode dealt with changing social roles as the Newcomers adapted to life on Earth. A binnaum has married a female and seeks the help of "his" male friend in reproducing (IIRC the binnaum was the one to help the male and his wife produce their own children years ago). The male is at first uncomfortable with this non-traditional situation (the male being an absent parent while the binnaum will raise the child), but eventually agrees.
River Song in Doctor Who is Amy and Rory's daughter, but because she was conceived on the TARDIS while in flight in the Time Vortex, she somehow has Time Lord DNA incorporated into her genetic makeup as well — enhanced by a little manipulation from the Silence. The TARDIS considers herself River's mother.
In Earth: Final Conflict Liam Kincaid is the result of three biological parents: two human parents and one alien. Agent Sandoval, Agent Beckett and Ha'Gel, who was possessing Sandoval.
In the Star TrekExpanded Universe, Andorians have four genders, two that approximate male, two that approximate female. Since they have a low birth rate, it's a Hand Wave for why that race isn't seen much in space, despite being one of the Federation's founding species.
The Mercedes Lackey song "Mis Conceptions" features a character who was apparently the result of a party with several mythological beasts as guests.
My mother never talks about that orgy And I can't really blame her much, although I would love to read the guest list for that party And if there's another like it let me know
Mythology and Legend
The Epic of Gilgamesh: Gilgamesh claimed to be "two thirds god, one third human", implying he had three parents. The Mesopotamians (and some other cultures) believed that if a woman slept with different men during or shortly before her pregnancy, that each of these men counted as a father. Thus the implication is that Gilgamesh's mom slept with at least two gods.
Heimdall, in Norse Mythology, has nine mothers. We do not get any further explanation as to how this works.
The Grekim from the RTSAchron have three genders (octo, pharo, and sepi). They also have three 'classes' (basic, pod class, and ligo class). Any two different genders can mate to produce a member of the third gender of the same class or the next one up. (E.g. a pharo and a sepi can produce an octo or an octopod, or an octopod and a pharopod can produce a sepipod or a sepiligo.) This is actually the species' primary method of producing units in the game.
William: The current known record for number of parents to a single child is twelve, and only nine of those were Uryuoms.
Gillian: That kid needed some serious counseling.
In Homestuck, the trolls reproduce by mixing the genetic material of thousands of different trolls together within the womb of a Mother Grub, who then gives birth to hundreds of thousands of grubs. As such, they have no taboos against homosexuality or incest, and why they even have separate genders is unlikely to ever be explained canonically.
The twist ending of one non-canon sidestory of Drowtales has Asira'malika Val'Jaal'darya cheerfully announce after teasing the (all female) clan leaders at a gathering about the identity of the baby she's carrying that they are all the child's mothers. The other leaders all either think this is a bad joke or get angry at her, but a montage showing the child growing up shows that she displays traits from their various bloodlines.
In the Justice League Unlimited finale Epilogue, it is reveal that Terry Mcginnis is more than just the son of Warren and Mary Mcginnis, but the biological son of Bruce Wayne thanks to Amanda Waller of CADMUS secret acquisition of Wayne's DNA in an attempt to create a Batman successor. Waller had Warren injected with Wayne DNA while claiming it was a flu shot. That injection overwrote Warren's reproductive genes. This last-minute Retcon actually helps explain why Terry, and by extension his younger brother, Matt, have black hair while Warren and Mary have red hair, when genetically their children should have been red haired too.
In Conway's Game of Life, a grid-based model of emergent complexity, a square will light up, becoming "alive", if it is surrounded by exactly three other "live" squares, i.e. "parents".
Polyspermy, in which two sperm penetrate a single egg simultaneously, can happen, even in humans. It's just incredibly rare, due to the egg's sperm-excluding cortical reaction, and the resulting triploid zygote cannot develop any further.
It is however possible for a woman who has released two eggs simultaneously to have them each fertilized by a different man. The two fertilized eggs, instead of producing fraternal twins, may then merge to form a chimera, ie. an individual that is a mixture of two different cell lines. Some tissues and organs would thus contain DNA from one father, while others would contain DNA from the second father. All tissues and organs would contain the mother's DNA, although not the same subset of her DNA. Thus this individual would have three biological parents. Chimeras made in the lab may have multiple "mothers" as well as "fathers".
There is an in-vitro fertilization (IVF) technique where the nucleus of one egg is inserted into a different donor's egg, then fertilized and implanted. The Mitochondrial DNA of the donor egg would be from a third person.
While ultimately, it's still one sperm per egg, some sex researchers postulate that this is the basis of promiscuous behavior among women, getting multiple men to inseminate them so that only the fittest sperm will fertilize the egg, thus ensuring your progeny will be prodigious.
A similar theory puts forth the idea that this is to create uncertainty as to who the father is, inspiring all the men it could possibly be to help support the woman and child on the off-chance it's theirs. It's still, of course, one egg and one sperm, but the resulting child would have many possible fathers.