My favorite reference might just be the Squall of Violence challenge for killing enemies with bladed guns, in reference to Squall and his Gunblade from FF8. And the fact that Flyboy mentions Bahamut when you're climbing his tower is pretty cool too.
And then there's the Sandhawk. The wiki says that the red text is a reference to some random named Errol Flynn, but I can't help but notice that the bullet pattern is a very slow flying bird. Harry Potter reference anyone?
The Weasley family owl was named Errol, and he was very old and slow. I'm convinced its a reference to him.
Some doors are best left closed, because once open, they're easy to walk through again and again. -- GT: Wretched Owls