Throwaway gags referring to Tron, including a lunchbox
The LOST references. Regina lives in house number 108, Apollo chocolate bars are seen countless times, the town clock in Storybrooke was stopped at 8.15h, the McCutcheon whiskey, Ajira Airways, and the number of actors who've been in both shows!
In the very first episode, we get to see a close-up of Emma's eye - done the exact same way these close-ups were done throughout LOST.
A Tinkerbell windmill becomes an important plot point
Possibly one to The Game Plan in the Pilot. A long lost child a parent had suddenly rings their doorbell, and introduces themselves as their son/daughter. In this case, both things are gender flipped from that movie.
We can add in Star Wars as Disney owns them now too. "In the Name of the Brother" has Greg's ringtone as the movie theme song, which is allowed to play long enough to become an obvious joke.
The same scene takes place hospital room "R2-42." In the alphabet, 4 corresponds to the letter "D," as in "R2-D2."
In "The Queen is Dead," Snow begs "Please, Mother Superior, you're our only hope."
A possible unintentional shout out occurs in the episode "The Doctor" in which Dr. Whale is revealed to be Dr. Frankenstein. Aside from the fact Whale's Storybrooke name references James Whale, the director of the first two Universal Frankenstein movies, the fantasy land version of the character briefly introduces himself as "The Doctor" and acts in a way that suggests a possible reference to the lead character of Doctor Who.
Henry's father, a nomadic petty crook, is named Neal Cassidy.
Also related to him: He's a thief named Neal who plans to give up his life of crime for something more stable and comfortable. Where have we heard that before? To reinforce the Shout Out, "Cassidy" even sounds a little like "Caffrey."
On the second season's tenth episode, Capt. Hook (who is an expy for Jack Sparrow) is seen standing atop his mast as his ship approaches bay, and then coming down with a rope. The way the scene is shot and the camera angles make it almost a dead ringer for Jack's famous entrance in Curse Of The Black Pearl (where he stands atop his mast as his ship approaches bay, then comes down with a rope).
The episode "Skin Deep" seems to throw up one of these every other minute. About a dozen all in all? [The names Belle and Gaston, Belle's father is named Moe French in Storybrooke (Beauty and the Beast was at first a sort of educational French tale), at least two of Belle's dresses are shoplifted right out of the Disney movie and so is her hair do, Belle's father calling Rumplestiltskin a "Beast", Belle being stuffed into a dungeon, "just an old woman selling roses", Belle being in that castle due to a deal to save her father (and others), True Love's Kiss (TM) changing Rumplestiltskin back into his non-cursed form, the chipped cup...
And from the same episode, another Disney Shout Out comes in the scene between Regina and Rumplestiltskin. Notice that strange blue hat behind Regina as she relates her story? The one with the yellow stars? Yep, that's the same hat from the Fantasia short, "The Sorcerer's Apprentice". Apparently Mickey really does exist in the Enchanted Forest, or at least the Sorcerer/Yen Sid/what have you.
The dwarfs are whistling the tune "Heigh Ho" from the original Snow White cartoon at the end of "Tiny".
A small one, but in "The Miller's Daughter", when Cora invades Gold's shop, Neal/Baelfire takes up a sword to stand alongside Prince Charming and Emma to defend Rumplestiltskin. The manner in which he holds his sword positively screams Kingdom Hearts (he holds the blade the same way Riku holds his Keyblade, as well as the same way Vanitas and Master Xehanort do), and given that Disney is a co-producer of the game, this is unsurprising.
In 3x01, The Heart of the Truest Believer has Neal explain to Mulan that those in the Land Without Magic believe that the people of The Enchanted Forest are just fairy tales, like legends and stories. This leads to the following dialog:
Captain Hook: Not long enough. You remember what I did to Rufio? It'll be a far worse fate for you.
Mulan tells Emma that if she does exactly as she says, Emma "might survive" - a line straight out of the Disney movie.
When Snow is living with the dwarfs, she hums "With A Smile and a Song" while wearing a red bow in her hair and cleaning the house.
In the pilot, Leroy (aka Grumpy) whistles "Whistle While You Work" in his jail cell at the beginning of a scene while Emma's in the next cell. He also whistles a few bars of Hi Ho when he meets Snow for the first time, also in jail. Apparently they're trying to work in the whole S Wat SD soundtrack. Which is fitting, since the show revolves around Snow's tale.
The shot where Emma and the gang get ready for a fight with the lost boys is lifted directly out of The Avengers.