That scene with Kyousuke near the end really got me. Key's stories usually manage that. But I'm gonna cheat a little and say To the Moon's ending hits me pretty hard because it hits close to home. I'm sure visual novel readers would like it.

I think I have been asked this question before... I said that Air was the saddest game, but little busters was a more emotional game. What I mean by that is Little Busters made me laugh cry and feel happy, it has the widest set of emotions. Little buster is one of my top favorite, I do not going to say favorite because I would have to compare LB! to other games that are not even remotely similar and that is silly.

The scene in refrain where Kyousuke explains everything... That has to be one off my favorate scenes in media in general, whenever may roles around I also tend to remember that I finished the game years ago.

And saddest vn? Apart from Little Busters, Kan Gao's game's are really good, as Kwhero mentioned, Mainly To the Moon & Finding Paradise. Though not sure if you could compare it to Little Busters.

I would say the entirety of Saya's route hit me pretty hard as much as Refrain did (or probably even more), since it gets much more personal on a degree compared to Refrain. It's like the same story but on a singular perspective with desperation that could be felt even more. (Spoilers ahead)

We see here a girl that was tossed into war zone ever since she was a kid who could never taste what childhood and adolescence should've been. She couldn't have had long-term friends and those that could be called friends were probably killed in terrorist raids and tribal wars in the places she's been. The only intimate friend she had was only for a day when she was in Japan. She was also killed pretty unfairly too.
When her soul found a place to get attached to, the virtual world in Little Busters, when she met her only friend again who she loved so much, she desperately jumped onto death after death, starting over each time she died with the difficulty arising in every reset. She wanted to feel his love, she wanted to live the adolscence she didn't have, and for that, she had to challenge against the mechanisms, the goals and the rules of the virtual world, even though she knew she was disrupting the world that welcomed her. And in the end, she had to take her own life to leave this world alone despite what awaits her after that is unknown.

I really can call Saya's route the best and the most dearly written story I've ever seen apart from the main story of Little Busters. It sheds light into the very things that I think what the majority of the people in our time lack: compassionate, loyal and never-ending love and people that's willing to defy anything with all the power they have for the people they love.

I really went back and forth a lot with Little Busters. At times I loved it, other times I thought it really dragged. But Refrain, hell yes, made it all worth it.