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).
Final Fantasy XIV has tons of them as well, especially in the side quests and FATEs. The localization teams do a stellar job sprinkling all sorts of references and nods to pop culture.
The Henry Stickmin Collection is a set of games that were on Newgrounds that is a choose your own adventure game with a ton of references to other things. From Marvel VS Capcom 2's Ironman Infinite combo to Jojo.
What do you mean legally distinct? You know that's Sam Lake, writer and creative director at Remedy, and face model for Max Payne 1/2, both also developed by Remedy?
I know. Rockstar acquired the rights to Max Payne at some point before releasing Max Payne 3. Remedy couldn't just include a character they didn't own, but they couldn't stop Sam Lake being Sam Lake either. Plus Casey being the knock-off of two out-of-universe characters is funny.
Evoland 2! Where the first game is mainly reference and no game, the second one is a completely original story and world which includes references. I highly recommend it.