The Brewing Hat is modeled after Vivian's hat, and the crows from the Owl express are a direct reference to the G-Men from Psychonauts. Plus Raz even makes a cameo in the attic of the mansion (at least in the beta, not sure about the full release). Snatcher is also a reference to the curse chests, he even gets stuffed into a box in the DLC and repeats some of the same dialogue when you check it. And of course there's all these obscure nods in textures and dialogue to other games like the first Metal Gear Solid. The Mario Sunshine stuff though is pretty obvious too.