In the campfire scene, replace the crown with Rapunzel's virginity. Mother Gothel tells her that Flynn is only after one thing and once he gets it, he will leave her.
Rapunzel's hair can also be seen as a symbol of her virginity, having gotten its power from a magic flower. Thus, Flynn "deflowered" her when he slashed her hair with a pointy object. It's even worse if you listen to the reprise of "Mother Knows Best" on the soundtrack. Without almost totally visual context, this is exactly what it sounds like.
This adds a even creepier factor to the Stabbington Brothers' "We want her" line. It's already pretty misinterpretable, but they want her 'magic hair', when they first wanted the 'crown'.
When Flynn tries to use "the smolder" on Rapunzel and it doesn't work, he remarks "This is kind of an off day for me, this usually doesn't happen," as if he were talking about something other than merely trying to charm a woman.
The scene where the Stabbington brothers encounter Rapunzel and try to capture her. The ominous atmosphere made it seem more like they were trying to rape her.
In Fantasia the alligators trying to eat the hippos and other female animals have a very suggestive looks in their eyes, and flirtatiously dance with their targets.
In Gnomeo and Juliet, the height of a gnome's hat seems to parallel with the size of something else. Made especially apparent when Nanette asks Juliet about the size of Gnomeo's hat, and when a jealous, small-hatted Tybalt deliberately smashes Benny's especially large hat.
When Mr. Incredible is out rescuing people from a burning building, Helen spots something on his collar and says, "Is that...rubble?" in the same tone of voice one would say "Is that lipstick?" His response goes with this too, in a terribly funny way: "It was just a little...workout. Just to stay loose!"
"It's time for their secret identity to become their only identity. Time for them to join us or go away." Also, Violet's dialogue during the dinner scene: "Normal? What do you know about normal? What does anyone in this family know about normal?! We act normal, I want to be normal!"
The scene depicting Esmeralda's dance from The Hunchback of Notre Dame. First she appears out of a puff of smoke onto a stage, then starts to perform a sultry dance, then runs up to Frollo, wraps her scarf around him and kisses him, then runs back onto the stage and continues her dance, then splits and winks at the viewer, revealing a brief closeup of her eyes, then gets back up and grabs a spear from one of the guards' hands, before finally driving said spear into the stage and dancing around it as if it was a pole!
At the end of the film, just right after Frollo falls to his doom, Quasimodo actually looks like if he is marrying Esmeralda (who, because of her almost being tried and sentenced to death by burning by Frollo for a crime she did not commit, is now left with a long, white dress since all of her other outfits were presumably destroyed by Frollo so that she would be executed properly before the trial) to Phoebus.
The final battle between Rourke and Milo at the end of Atlantis The Lost Empire is reminiscent of a bully beating up a nerd. Guess which is which!
When Ariel is first transformed into a human and swims up to the surface, she bursts from the waves gasping for breath, nude but for her Seashell Bra, her head flung back, her back arched, looking for all the world as if she were having an orgasm. Since the entire story can be interpreted as a metaphor for a young girl becoming a woman and discovering her sexuality, and the potential perils of love and sex, this may very well have been intentional.
Ursula, while not a good character, was sane and composed during most of the film. However, when she transforms into Vanessa, its implied that she lost quite a bit of sanity (to the point of becoming a borderline Ax-Crazy) when turning into her, as she talks to her mirror in a manner similar to a schizophrenic, emits a psychotic grin when throwing a pin at a mirror's head with enough velocity to knock the mirror back, and most certainly kill a person had that been a human being, not to mention her cackling.
The scene where Triton argues with Ariel in her grotto then destroying it is scary enough, but just listen to it in a...different context.
Tulio really gets into that massage he gives Chel, and they were quite clearly having sex when Tzekel-Kan walked in on them.
Batman Beyond: Return of the Joker features this with The Joker and his Foe Yay with Batman leading to a scene where he corners Batman in his batcave, throws him into a chair, and leans over him while getting really close to his face with a rape face.
Vanellope's glitching is treated like some sort of disease or illness, similar to epilepsy or Parkinson's Disease by the other racers. She even refers to it as "pix-lexia" and mentions that she was mistake and that she wasn't supposed to exist.
The entire scene with the other Sugar Rush racers picking on Vanellope and destroying her race car is basically playground bullying at recess.
The dialogue for the Laffy Taffy scene sounds like something from a bad S&M porno when taken out of context.
The scene where Ralph wrecks Vanellope's cart is heartbreaking enough, but listen to it out of context and it sounds like child abuse...and not the humorous kind.
Ralph being "randomly" stopped and questioned by the Surge Protector constantly, coupled with him being treated badly for being a "villain", closely resembles racial profiling in airports.
The infamous scene from Pinocchio and the Emperor of the Night where Puppetino turns Pinocchio back into a lifeless puppet has been compared to a rape scene, which must have been why the scene is altered/cut on TV showings.
Prince Hans is textbook example of an abuser, complete with crafting a socially acceptable facade, using the "honeymoon" period of pretend affection to gain his victim's trust, then turning nasty once he's in control and gets what he wants. The opening song spells this out pretty succinctly: "Beware the frozen heart".
The way Elsa's parents treat her - keeping her a secret and locking her away from the world, despite how clearly it makes her miserable - is depressingly similar to how a lot of parents treat children who aren't "normal", especially disabled children.
Elsa is forced to keep a secret that she will be shunned for. Later, it all comes spilling out and she sings "Let it Go", a song about being who she is without caring about what others think of her. If you didn't know she was hiding her ice powers, that could easily be a story of a girl coming to terms with her homosexuality.
Memphis' confession that he dropped Mumble when he was an egg in Happy Feet, thus explaining why he's "different", can be just like somebody saying that his child was dropped on his head when he was an infant.