In the dub of episode 10 Gaomon's casual remark of Marcus being run over by a car and being squashed by an oil tanker.
Digimon Savers has one that's a callback to Adventure, or rather the first movie: Koromon's first action upon hatching is to latch onto Masaru's head!
Marcus in the dub of the semifinal episode: "King Drasil is a PC?!" Probably not meant to be funny, but it caused a lot of "Digimon runs on Windows" jokes.
Half of what Lalamon says about Yoshi.
Agumon and his digimon pals were in a glass box cage. His solution for breaking out? Use Pepper Breath inside, the way his pals reacted were priceless.
The sketch of Kurata in Episode 31.
Outtakes featured during the credits of the movie. At one point, Algomon falls from his perch after catching on fire himself.
Kristy's and Thomas' reactions to the unspecified scare in Episode 7, mainly in how opposite they treat it. Thomas, the teen who fights otherworldly monsters without flinching or psychological damage, was visibly panicking. Kristy? She was having an absolute blast.
Earlier in the same episode, after Kristy stomps Thomas at an arcade game, Gaomon tries to lighten the mood that at least Kristy isn't like her brother. Thomas responds that she's exactly like her brother with how she derails his plans.
In the Japanese version of episode 31, when Masaru and Ikuto deal with a swarm of Gizumon XTs:
Masaru: All right, that's gotta be all of 'em this time.