When encountering the electric seaweed, Fugitoid says he'll get them through it in "two minutes and twenty seconds", the same amount of time you have to complete the electric seaweed level of the first TMNT game.
This marks the second time Greg Cripes (Michelangelo) and Ron Pearlman(Armaggon) work together in an animated. The othwr series being Teen Titans. Greg Cripes as Beast Boy and Ron Pearlman as Slade.
The electric seaweed in this episode might be a reference to the seaweed from the original TMNT video game on the Nintendo.
When Miley is saying goodbye to the Daagon guards he calls them Mer-Dudes. Mer-dude was actually a toy in the original TMNT toy line and as such the designs for the guards were heavily based on it.
When the Cthugga is chasing the Ulixes in the cave and tries to "chomp" the spacecraft, this is a reference to the Exogorth (space slug) trying to "chomp" the Millennium Falcon in Star Wars Episode V: The Empire Strikes Back.