Yolei's "Mimi fantasy," in which Mimi suddenly has blue eyes so that she looks more like Utena.
The Dark Ocean and Dagomon, to the Cthulhu Mythos (the episode was written by Chiaki Konaka, who actually has written Cthulhu Mythos stories).
Diablomon Strikes Back has Armageddemon, whose appearance is reminiscent of an Angel. Furthermore, when Omegamon is severely wounded in the battle, he is left standing up with his arms having fallen off in a pose that echoes Unit 02 after being defeated by Zeruel.
There is a quick blink-and-you-miss-it shout out in episode 15; when ShogunGekomon sees the dark tower erected, he cries out "GeGeGe no Ge!"
A cool reference to catch after watching Interstellar: during the final episode, as Malomyotismon covers both worlds in darkness, he boasts, "The dying of the light, and no one to rage against it!" This is a reference to Dylan Thomas's poem, "Do not go gentle into that good night."