Pretty much every movie ever has deleted scenes, but sometimes even though the scene is deleted, lines or scenes referencing ultimately cut material remain in the final movie. Sometimes the references remain due to an oversight, but it could also because the reference is part of a longer piece of dialogue or plot and it would be impractical to edit it out without reshoots.
For example, in The Wizard of Oz, the Wicked Witch of the West tells her monkeys that Dorothy's friends won't be any trouble because she's "sent a little insect on ahead to take the fight out of them." This is a reference to a scene that was ultimately cut where the Jitterbug would sting the main characters and force them to dance the jitterbug (this is also where they were going to lose their weapons).
Storm's infamous "what happens to a toad when it gets struck by lightning" line from the first X-Men movie was originally meant to be the payoff to a running gag where Toad would keep boasting about "what happens to a toad when..." but all of those lines were cut so we're just left with a weird scene.
So what other movies have lines or scenes referencing deleted material?