Something that totally shocked you learning it or realizing it. I might be using the wrong wording here, but ill give you my example:
In Ocarina of Time, we all know the Triforce was cut, or otherwise not something you get in the game, save for in the cutscenes towards the end. BUT - did you know you can actually go find it and see it in the game?
If you have a Gameshark, turn on the levitation code. Go go Zeldas Cortyard in the room where she is, and fly over the wall. When you fall, you'll land in a pool of invisible water, and underneath the center of the room with the flowers, look down - there it is. Can't interact with it, but you can see it, and i choose to believe putting it in that exact spot was intentional for lore reasons.
What do you got?
In UFO 50, the characters Amy and Alpha are the same person.
Amy traps her little sister in the back room so she can throw a party (Party House + Mini & Max). Mini helps the Mol Duk civilization of mold-people, and hears their prophecy that they'll become a technologically advanced people (Mini & Max). An unnamed friend of Amy gets kidnapped by a man who has become an infested mold zombie after drinking Mol Duk tea (Night Manor) given to him by a therapist (probably one of the counselors from Party House). Amy and friends fight a zombie apocalypse, get abducted by aliens, beat up the aliens, and continue their journey, presumably keeping the flying saucer (Fist Hell). The Mol Duk people become Woogie's species (Onion Delivery; yes it was Earth all along). Amy escapes the planet using the space ship, then goes on a series of adventures under a new assumed name, Alpha (Velgress, Overbold, Pingolf, Quibble Race). Further evidence for this is that both Amy and Alpha have wildly inconsistent hair color from game to game.