Addams Family Values: Wednesday and Pugsley are forced to watch various family movies, including Annie, at summer camp.
Austin Powers in Goldmember: When Dr. Evil and Mini-Me are in prison, they and their fellow inmates perform a ghetto remix of "It's a Hard-Knock Life".
Bad Teacher: The school puts on a production of Annie; Amy complains about the disappearance of the Annie wig and laments "The sun will not come out tomorrow". Coincidentally, Cameron Diaz would go on to play Miss Hannigan in the 2014 film version.
Deadpool 2 has Alicia Morton's rendition of "Tomorrow" playing in flashback scenes where Cable's family was killed, and in the film's climax.
Junie B. Jones is a Party Animal: When Junie B and her friends play a Cinderella-themed dress-up game, she refuses the role of Cinderella's Ugly Stepsister, and instead volunteers to sing songs from Annie at the ball.
In And Shine Heaven Now, a now adult Annie (going by Ann) has taken over Daddy Warbucks's business of arms dealing, and provides Integra and co. with new weapons. (Notably, thanks to the Comic-Book Time explanation on the main page, she only appears to be in her thirties in roughly 1999, much to Pip's delight.)
A sketch from "Snarfer Image" features Annie bring considered for adoption by a couple. Here, it's revealed that she was a child sex slave and has multiple personalities (including Pippi Longstocking and Oliver Twist).
Tiny Toon Adventures: Near the end of "Whale's Tales", Gotcha Grabmore is forced to listen to a group of singing octopus pirates, the leader of whom asks "Would you rather they do the theme from Annie?"
Billboards and posters for "Fannie", a thinly-veiled (and, knowing Rockstar Games, crudely named) reference to the musical, can be seen throughout Liberty City in Grand Theft Auto III. The Liberty Tree website made by Rockstar to promote the game made it even clear about the work they were (passively) parodying, with theatre correspondent Morgan Merryweather describing the play as a "happy tale of a young girl who is definitely a real red head."
The Harbucks household in the Golden Era-themed Roaring Heights neighbourhood for The Sims 3 is a thinly veiled reference to the Annie mythos, with Olivier Harbucks and Shirley Templeton as its members. Shirley also doubles as a reference to Shirley Temple, though while both Annie and Shirley do have curly hair, Temple never appeared in any Annie adaptations contrary to what some may think.