Earth's capital city is run by an oppressive government that uses Ninja Robots to instill fear into the people (those who saw the ending of The Ninja Warriors Again will notice something similar) ... and the background music played when battling them is Daddy Mulk, from The Ninja Warriors.
The Roader enemies share the same name and attack pattern as the Roader enemies from Mega Man.
BlackTech are not just weak to holy attacks, but also Ki Attacks. Another Pokemon type reference- Fighting beats Dark.
Shark tells your character "I'm bigger than you and higher up the food chain!" Another boss, this one with a black hole for his body, shouts "GET IN MY BELLY!!!" when he does his Limit Break to suck you in.
The Lock-on Homing Laser weapon (the strong one used by Raybombers, not the weaker ones) is similar to that of the RAY Series. You have to lock onto enemies to use it. The laser colour changes from blue to green to red as its strength increases, similar to Ray Force, while the lock-on reticule is like that of Ray Storm.
The Gunwhale boss is first seen being carried by eight flying bird-like robots, similar to the Twitter Fail Whale. Plus, it looks very similar to Great Thing.
After Raysilon defeats Epsilon, he says "You left me no choice, brother". Note that both of them are actually two of three similar beings, so they can be considered brothers of sorts.
A speedboat Giant Mook has an attack called Hydro Thunder Hurricane, where it shoots out a huge electrified water tornado out of its motor that does water-, lightning- and wind- elemental damage.
The Monster Compendium section has a bit of trivia and silly facts about the enemies, including "rejected names" for baddies. Some of the rejected names are Shout Outs to other works, usually because said names would infringe on copyrights or are outright joke names.