Well, goodness, I have completely forgotten a few more references on Once Upon a Time, so here is an addendum to my previous post!
Rumple and Belle echo a conversation between Belle and the Beast about the dungeon being her room (Only the Beast leads her out of it while Rumple leads her to it).
There is a clock, a candelabra, and a teapot in the background during the "Skin Deep" episode.
Archie's dog is named Pongo for Pongo of 101 Dalmations.
The magic mirror is blue like the genie from Aladdin and that episode specifically mentions the kingdom of Agrabah.
Personally, I'd love to see an episode in which the characters directly reference their Disney counterparts!