>>712539004
>Villain can become an optional recruitable ally
Chrono Trigger does this. If they're a villain who just joins later, it doesn't count, it must be optional.
>>712539114
Paper Mario Thousand Year Does this great.
>>712539991
Pokemon Violet and Scarlet go hard on the leitmotif. From the early game to mid game to end game, the main theme is always part of most major tracks.
>>712540128
I personally don't like it, Nier Automata did it "best" because it's require to do unlock the best third route end in the decision branch.
>>712540320
Persona games do this well.

My favorite trope would have to be horror games/movies "diaries/recordings" from people who are obviously going to die. In real life it wouldn't make sense, but they're charming enough that they get a pass. Dead Space has tons of them that make you laugh or feel unnerve.