Family Guy did an incest joke about Donnie and Marie.
In a recent episode, Meg asks Chris if he wants to "practice kissing again." Chris didn't even bat an eye.
And in the movie, Lois complains to Peter that, with Chris and Meg around, they have no privacy at all and asks if they shouldn't be dating by now. Of course Peter assumes she meant dating each other.
In the episode "Halloween on Spooner Street", Meg and Chris in costume make out in a dark closet not knowing who the other is until the door is opened. They're both horrified with Meg screaming that they "did so much". However, they try to make light of it later. Chris knew what costume Meg was wearing, but being Chris, he had probably forgotten.
Even weirder: Meg's dialogue suggests that upon reflection she might not be averse to the thought of doing it again, even going all the way with Chris. He, however, tells her, "Don't count on it."
"Fresh Heir" reveals that they bathe together, a fact they keep secret from their parents
Seahorse Seashell Party implies that Chris might have had a change of heart.
Road To Rhode Island contains this exchange:
Farmer: I don't trust you, you put your seed in my daughter's belly, you're fired!
Worker: But Pa, you can't fire me!
Farmer: You're lucky you're my brother too or else I'd kill you!
In The Transformers, Orion Pax and Ariel were originally boyfriend and girlfriend. After their bodies were destroyed, Alpha Trion recreated them both as Optimus Prime and Elita One and the two continued the relationship in their new lives. Their anatomy turned out to be so similar that Optimus is able to save Elita's life with an energy transfer, and Optimus seemed a bit taken aback when Alpha Trion told them about their origins. When she steps close to him at the end, he even walks away quickly. No one outright mentions the word "incest", but it's heavily implied that something weird's going on.
"Something weird is going on" is that Optimus had forgotten who his creator was so it's more surprise that he's learned Alpha is his deadbeat dad. Also Elita was leaning in for a kiss so it may be more "hero denying his pleasures" than anything else. Also two reasons he denied her: parents' anger at robots kissing and kids' reaction to seeing a parental (albeit fictional) figure smooching other than a quick peck on the cheek.
In South Park, there is an episode in which Stan has problems with his older sister, Shelly, who constantly beats him. When he asks his friends' help, Kenny suggests something through his orange parka. Although his words are muffled, the suggestion is obvious, because Stan replies, scandalized: "Sick dude, she's my sister!"
Kyle suggests that Stan use The Power of Love to stop her, just saying "Shelley, you're my sister and I love you..." the next time she tries to beat him; Kenny then finishes Kyle's sentence with "...and I want to take off your bra."
One episode had a brother and sister news crew, Tom and Tammy Thompson, as lovers.
In American Dad!, in the Episode "Stannie Get Your Gun," Roger tricks Steve into believing he's adopted. This triggers a bit of a Heroic BSOD in Steve and one of the first things he does is go to his sister Hayley, says there's always been "sexual tension" between them, then makes out with her. Hayley is understandably surprised and repulsed. Roger didn't intend it to happen, but he's not complaining either. ("Anything that happens after this point is gravy.")
In the episode "Meter Made," Roger paints a nude picture of Hayley (who was posing for an art class) and starts loaning it to Steve for use as masturbation material. In Steve's defense, he didn't know it was Hayley (the painting stops just above her lips) and he's completely Squicked out when Roger lets it slip. Likewise, Hayley never actually blames Steve and is just as angry over Roger screwing with the poor boy's head as she is over him selling her nude image in the first place.
In the episode "An Apocalypse to Remember," the Smiths are invited to a party celebrating ethnic minorities in America. Unfortunately, due to Stan misreading the invitation, the family turn up wearing blackface make-up and the Smiths are forced to leave, embarrassed and angry. At the car this dialogue takes place:
Steve: What a boob.
Stan: What was that, Steve?
Steve: Um, I, uh... asked Hayley if I could squeeze her boob.
A reference to the fact that Milhouse's parents look extremely alike. Aside from Milhouse, they're the only naturally blue-haired characters in the series. (Marge dyes, to maintain the naturally blue hair colour she had in her youth. Although in one episode it was revealed she didn't know she'd gone grey, and her hairdresser had been dyeing her hair back to blue for years, with the smell of the chemicals giving her repeated short-term amnesia over the matter.)
Also Chief Wiggum and his wife Sarah, who look like each other and share mannerisms and accents. Like the Van Houtens, they also have blue hair.
Future Rod and Tod Flanders seem to be lovers.
In the episode "Kill the Alligator and Run", the Simpson family flees from the authorities of the state of Florida. The family ends up working in a restaurant and they live in a trailer. So you get this scene:
Homer: Yep, this place is great, and someday when Lisa and Bart get married it will all be theirs.
Marge: You mean when they marry other people.
Homer: OK... but I'm not paying for two weddings.
In the episode "Little Girl in the Big Ten", Lisa speaks with a college girl (Carrie), and Lisa almost admits that thinks Bart is cute.
Lisa: I share a house with a couple of girls, couple of guys.
Carrie: Guys, huh? Are they cute?
Lisa: Well, Bart's kinda—- NO!
Aversion: With the communal raising of children the titular species employs in Gargoyles, this was an early fan idea about Demona's and Goliath's relationship, until Word of God severely beat that out of the fandom by stating that the pheromones a gargoyle releases when he is courting smell horrible to any close family relation. This is only natural, really, since nature prefers genetic diversity over in-breeding.
Interestingly, gargoyles still consider the other gargoyles they were raised with to be their siblings, but coupling inside this social family appears to be perfectly normal simply because if they had already evolved a physical mechanism to prevent inbreeding (the pheremones), then there'd be no pressing advantage to evolving a psychological mechanism (Westermarck Effect — the origin of the incest taboo).
The titular characters from The Twins of Destiny had this implied, through their interaction throughout the series but mostly their decision in the final episode to leave everyone else and everything they have bonds with behind to be together. Just for the record: Jules and Julie both have a different set of parents, but their mothers are implied to have been incarnations of the Moon Goddess. Their mothers died during the twins' birth and their fathers were taken prisoner by the Empress of China, who wanted the twins dead. Jules and Julie were smuggled out of the country and brought to France, where they were raised by one man as siblings until they were about 14 years old. They know they aren't biologically related, but they do consider themselves siblings, often referring to the other with "my brother" or "my sister".
An episode of King of the Hill had Bill meet and fall in love with a beautiful single mother named Charlene. Dale, suspicious of her daughter, does a DNA test and discovers that she has the same paternal DNA as Joseph, which means they're both Chocolate Babies fathered by John Redcorn. When Hank tells Peggy, she freaks out because the two kids have been getting very close and sends Bobby off to play fifth wheel and prevent anything really Squicky from happening. In the end, the Hills convince Redcorn to seduce Charlene away from Bill, leading to her moving away.
101 Dalmatians The Series had Two-Tone and Lucky as love interests. They're siblings, though it's never mentioned, and to make matters worse they're not supposed to be Not Blood Siblings; they were of the original 12 pups. It's possible the show did change their bond or the writers assumed she was adopted.