The Dust Zone arc uses the words "GIGA DRILL BREAK" a lot.
TENGEN TOPPA: SHOU-CUTEMON!!
Chapter 28 confirms it with GURREN LAGANN: XROS FIVE.
A Lopmon named Nia in Vampire Land to Cutemon's name of Simon. Naturally, anyone who has seen the anime would expect her to die at the end of the arc because of this naming. She doesn't.
Marcus makes several references to and comments about Portal 2, and Space Core makes an appearance inside the Static void, directing Xros Heart back to earth when they try to open a portal.
In Magma Zone, Shoutmon urges Taiki to "Do the Windy Thing!"
The four Guardians of the Digital World, Hephaestus, Cetus, Echidna, and Typheus, are the Denizens of Dave, Rose, Jade, and John respectively.
Following off of this, this whole universe seems to be the result of a modified SBURB game.
Taiki first uses Hephaestus' power to create music out of thin air: the song MeGaLoVania, to be exact.
The second half of Dust Zone's arc features the above, as well as two other songs (Umbral Ultimatum and Descend) from Homestuck.
Infinity Mechanism is used as the opening for Chapter 31.
A Pawn-Chessmon goes by "Problem-Chessmon" and "Problem Sleuth." The Red Pickmon is drawn like a certain Ace as well, in one of the author's drawings.
Another Pawn-Chessmon is named Terezie. A third is named Kroket, a Stealth Pun the author came up with, stemming from Crocker > Croket > Kroket, in reference to Jane Crocker.
What Scarf? You are quite sure there has never been nor never will be any scarf!
Two Pucchiemon are named Rose and Jade.
The red Monitamon trio of Eridan, Aradia, and Sollux.
The randomness that the Falcomon chasing after Problem-Chessmon shouts is from Problem Sleuth.
'Riska' the Dracomon has Eight Eyes like a certain Spider Troll.
One of her new attacks is "MeGaLoVania" to hammer the point home.