More of a playable story, but the entirety of Dear Esther is a bit heart wrenching.

Stray ending

Apollo 11 VR. I would be amazed if it's a common response as most folks would probably just think of it as a very boring simulated rollercoaster. For me it produced an overwhelming feeling of awe as I reflected on humanity's path to that point and the enormity of lifting off from our little blue pearl.

I got all fucked up inside when Agro died in Shadow of the Colossus.

Fallout: New Vegas.

At the end of Boone's companion quest, we're watching the sunrise, having barely survived the night. He confesses what really happened to his wife. Nat King Cole comes on the radio with "Love Me." I weep.

Borderlands 2, the ending of the Tiny Tina DLC.

Damn near everything in Nier Gestalt/Replicant. That game wrecks me every time I play it.

There have actually been a lot of games that have made me cry over they years. Some of the ones I remember are:

Metal Gear Solid 1, 2, 3 and Peace Walker

Kingdom Hearts 1, 2, BBS, Re:Coded and 358/2 days

Final Fantasy 10 and (obviously) Crisis Core

Castlevania Order of Ecclesia

I'm pretty sure there are more but I can't really remember any others. I've kind of always been very sensitive to emotional things, so a lot of games get at least a tear or two but the ones I mentioned were games that I remember being wrecked after playing.

Mafia 1. "Mr. Salieri sends his regards". Need I say more?

The first time was in Mass Effect 3, when Liara shows you her project in your cabin. For me, this was the first time in the trilogy where I felt that we could really lose the war against the reapers.

Another very good moment was in Life is Strange Before the Storm, when Chloe finds her dad's car in the junkyard. That hit hard.

Mass Effect 3: "Leaving Earth"

Brothers. Damn ending making me feel empty…

Life is strange. Repeatedly.

I was pretty emotionally stunted and depressed as a teenager and had trouble crying even when I wanted to (it's a horrible feeling, physically) so Earthbound and Mother 3 were therapeutic

No spoilers but the ending of Life Is Strange made me cry.

Shane’s 6-heart cutscene on the cliff in Stardew Valley.

Also the very last story moments of Tears of the Kingdom. The dive reach grab bit.

The ending of Legend of Zelda Tears of the Kingdom, it was just so cool and and so well done. What a great final boss when compared to Breath of the wild.

I tried to install Skyrim and my disc was unreadable

ME:3 and the cliff.

Several points in Life is Strange, I have yet to finish that game.

FFXIV, over and over. The kind of nobility and self sacrifice displayed in that story has set me crying several times. Honestly, I can feel it a little bit just thinking of some of those moments, but I try to smile through it.

Because a smile better suits a hero.

Hl2 EP2's ending

The entire "What Remains of Edith Finch" game

Pretty much everything in The Last of Us Part 1 & 2.

Ori and the Will of the Wisps has some great emotional moments that are complemented by a fantastic soundtrack. Learning about Shriek's backstory after being hunted by her the entire game was just too much.

Have probably done that over a bunch of games over the years but can't remember much of them but the one game that immediately comes to mind is spiritfarer. Had so many touching farewells and some of them were too relatable to be not shed a tear. Man Atul left me speechless for days, I still need more hugs.

the end of season 1 of the walking dead game. goddamn what a gut punch

A weird one that I've not seen mentioned: the intro to Battlefield 1. It is really well crafted and was emotional in a way I've never felt from a war FPS.

The multiple unavoidable deaths and brief epitaph shown on screen, before hot swapping to the next soldier felt poignant. Really hit me with the pointlessness and futility of WWI, the plight of the common soldier and the sheer scale of death.

Getting the True Ending in the base game of Outer Wilds. Including the credits, including after the credits. So beautifully bittersweet.