Mine:
Mayuri’s ending in Steins;Gate My Darling’s Embrace: As one of the rare Okabe/Mayuri shippers, finishing my S;G experience with this is one of the best story payoffs I experienced.
Tomoyo After true ending: Very heartbreaking and IMO much better than the canon Clannad After Story ending. If I have infinite money, I’ll have an anime produced out of it.
I think for a branching / multiple endings game, the first route will always be the most special. Because at that point you’ll be going in blind, to some extent. You may understand the vibe of the beginning of the game, and can extrapolate on the tone of the endings, but you’ll never know for sure until you complete the route. You’re forced to prepare yourself for the tonal shift that may or may not happen. And from that uncertainty comes a better payoff, in my mind.
For that reason I’ll nominate my first ending of Grisaia no Kajitsu, Sachi.