In "Rise of the Turtles, Part 2", the Turtles find a canister of mutagen. Mikey suggests that they drink it and reasons that if you mutate a mutant, you get a super mutant. That's exactly what happens when Dogpound takes a mutagen bath and turns into Rahzar.
In "The Gauntlet", Leo refers to the Turtles as Mighty Mutants. Guess who shows up in the third season? The Mighty Mutanimals. Also, they were investigating one of the group's future members, who in this case is Pigeon Pete.
At the end of "Metalhead", Donatello considers tricking out his bo staff out with various gadgets and a missile launcher. Sounds an awful lot like the bo staff his 2018-counterpart uses.
After Leo develops a crush on Karai, he goes to April to talk about it. April is initially on board with it until she finds out Leo's Love Interest is in the Foot clan. Then, in Teenage Mutant Ninja Turtles: Mutant Mayhem, Leo has a crush on April herself. So now April flipping out seems appropriate for different reasons.
In "Plan 10", Casey and April switch each other's mind during a battle at the Technodrome, and Casey even admits liking being a girl. And then comes Rise of the Teenage Mutant Ninja Turtles, where Casey is portrayed as a girl.
In "The Manhattan Project", April calls Karai a witch. Following the latter's Heel–Face Turn, Karai partners with witch girl Shinigami.
In order to fight Kavaxas, Donatello invents what are basically proton packs. The IDW series actually had an official Crossover with Ghostbusters a couple years before this story.
A training simulation has the Turtles riffing on Street Fighter and Mortal Kombat. The following year the Turtles were announced as Guest Fighters for Injustice 2 which isn't just made by the same company that makes Mortal Kombat but also features guest characters from the series. The Turtles would later appear as skins in Brawlhalla, which also features Street Fighter characters and skins of Street Fighter characters in Street Fighter 6.
The "Mutant Apocalypse" three-parter shows Raph's future self having bulked up considerably and with a full-head bandana. His design in Rise of the Teenage Mutant Ninja Turtles (which was announced months ahead of the three-parter's airing) has those exact signature aspects. What's more, he's the acting leader!
That said, the bulked up, full-head bandana wearing Raphael actually predates this version, as that design was also used for the Michael Bayproduced movies. However, this version being the leader was original concept invented by this series.
