Gearbox Software is simply... AWESOME! They made several homages to the following video games: Dark Souls, Metal Gear Solid and Minecraft.
Dark Souls: http://imgur.com/a/IXla3
Metal Gear Solid: Not only you return to a familiar place (Fyrestone), there's an enemy boss that bears a resemblance to Metal Gear Rex (boss name: Saturn). There are also several customization items that make reference to Metal Gear Solid (such as Metal Fear, a head skin that looks awful similar to Gray Fox's helmet).