Spoiler: Don't open Honestly, I cried everytime when you or you're Partner had to leave the Pokémon world. Spoiler: Psmd Spoiler. But my best Moment was in Psmd: as Nuzleaf sent me to school although he believed me that I am a human. And he ist one of the bad guys too .
My favorite PMD moments are the ones with Grovyle. He was cool and a great character with some really good moments. He had a great Special Episode and I'll never forget him.
The ending at every single PMD game would put tears in my eyes. Even if the plot was totally sloppy (looking at you, GTI), I can at least count on the ending to make the most significant impact on me.
Quite different from what others would say, but what I really loved from PMD besides plot and game mechanics is the music. Every time I hear the farewell songs, it (almost) moves me to tears. For the plot, I love the way everything that happens has its purpose, one way or another, that leads to the final plot. I especially like the plot of PMD Red, where you had to leave Pokémon Square to prove your innocence, and how your partner still remained by your side the entire time.
For me, it's always the end of the PMD main storylines (except for SPMD), because: Spoiler I always have hardcore feels (yes I am a sap and I'm completely aware of that) at the end of most of the PMD games when the avatar 'dies' and stuff only for the avatar to be reunited with the partner afterwards. ...Though I do admit to crying a little at the end of SPMD because I totally didn't see that ending coming at all.
My favourite part of any of the PMD games is in the postgame of Explorers. You and your partner have settled down and gone to sleep after a long day exploring when Palkia pops out of nowhere and drags you into another dimension. It might not have the feels of my other favourite scenes, but something about how abrupt the whole thing is just makes me chuckle every time I think of it.
My favorite moment in PMD EoS... Spoiler It's when Grovyle tackles Dusnoir to go back to the future. It's so touching and I love that Grovyle does it all for the sake of everyone in the future, even if his best friend in the world won't remember him. I love the selflessness and how Dusnoir after being such a pain is taken down.