Sins of the Fathers Chapter 9: Tombstone - S3-E9
Trivia: When Spider-Man saves Tombstone from falling into a bubbling vat he jokes about him coming out with "green hair." Clearly that's a joke referencing DC comics' Joker.
Behold the Negative Zone - S1-E12
Trivia: When Blastaar comes through the Negative Zone into the Earth dimension, Thing remarks that Blastaar makes him look like Brian Austin Green. Brian Austin Green was the voice of Human Torch for the first season of this show. (00:11:18)
Trivia: The song playing on the radio when Rosebud breaks in, 'I'd Take a Bite of the Moon For You,' references the episodes 'Alone Together' and 'Tick Vs. Chairface Chippendale.' The song playing when El Seed breaks into the botanical gardens is a jazzy version of the show's theme song.