The binding of Isaac has shit ton of them.
Do old build-engine shooters like Blood, Duke Nukem 3D, Shadow Warrior, etc count?
Sapienza, Italy in Hitman has outfits for red and green plumbers.
Sam and Max has references to all kinds of things.
Hypnospace Outlaw has a ton of references to pre-y2k pop culture.
Power Wash simulator has a number of official crossovers with IPs like SpongeBob, Warhammer, Laura Croft, Final Fantasy VII, etc. (oh shit I just checked and there's a Shrek one coming out soon).