Not asking for the most successful or even worst. The quality of the game doesn't matter. Just really surprising crossovers.
I will give two examples.
The Witcher 3 X Daemon X Machina
If unfamiliar with DXM it's an Anime Japanese mecha game. Like a mix between Armored Core and Zone of the Enders. While this game has some anime crossover stuff. That's expected. The strangest is The Witcher 3. This game has a heavy create a character mode to Geralt and Siri is not in the game directly. Just you can make your avatar look just like them. Either way very strange. If you ever wanted Geralt piloting a mech. here you go!
Dante. Shin Megami Tensei III. More people probably know the meme than the game itself. This is where "Featuring Dante from Devil May Cry" came from. While it does make sense in the universe. Dante fights demons as do you. Just it happened purely on a handshake deal. Dante in SMT while an SMT artist-designed Dante's Devil Trigger in DMC3. Atlus and Capcom.