The FATE chain in the Dravanian Hinterlands: "Metal Gears Rising" to "Metal Gears Revengeance" and culminates in "Metal Gears Reveangance 2" in which you fight a giant Vangob machine. It's a pretty obvious reference, heh.

The big FATE "We Fought a Dzu" is a reference to the Matt Damon movie, "We Bought a Zoo".

"Prey Online", the world FATE in Azys Lla is, I think, a reference to Sony's Play Online feature for the PS2.