Tomoyo After and AIR were close for the story as a whole. I voted Tomoyo After because I didn’t see that ending coming, whereas I expected the ending for AIR to be approximately what it was on my first play through.
I’ve decided to disqualify planetarian from my list of candidates due to being a kinetic novel. The lack of choice means that you as a player can’t experience the futility of making choices that won’t affect anything. Being aware from the onset that there aren’t any choices at all somewhat diminishes the impact IMO. (Planetarian was really great though.)
LB! and others don’t apply for me because they all have happy endings. However, among these, I have to say that LB! did get the most feels from me. Especially during refrain… Just wow. Shizuru’s route in Rewrite was also really great for that. (The other routes didn’t affect me nearly as much as hers though, so not Rewrite.)
AB! is… well, I’d rather wait until playing 1st Beat before deciding. I only cried once, at the end, while watching AB!. Otherwise it was just a bit depressing. (Pacing problems diminishing the effectiveness of the story, probably.)