I’d recommend your own one @Havenstone, the first one can already end somewhat tragically and it is only going to get, much, much worse before it gets any better if it gets any better. The grim reality of rebellion I suppose, in my mc’s case also compounded with trying to build a brave new world from and on the ashes of the old.
In the end I envision even the better endings my mc’s rebellion could get as very much bittersweet.
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Choice of Robot, A Study in Steampunk and Way Walkers: University. 
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Wow I’ve seen so many works on here that I’ve played but never realized those types of endings because I always choose the charm/magic options consistently (it’s what my characters do and I genuinely enjoy doing it) and thus getting “normal/good” endings.
Time to replay a few of these haha
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Oh god do not remind me of that game. In the almost 2 hour let’s play I watched of it, I cried 4 separate times, like a baby. That’s definitely the winner for me.
As for my picks on the topic, I don’t think I’ve played a CoG/HG that really got me yet. There is another IF, though, that hit me really hard. Bi Lines from this year’s IFComp. I’m not sure if “sad” is the right word, because while I enjoyed it and thought it was well-done (save for a couple parts I thought could be better, but given it was made in 5 days, I’m letting those slide), it was more painful for me than sad. Being a male sexual assault survivor myself, it was… a lot. My situation is completely different (my assault was not remotely the same as the protagonist’s and I’m not a bi man in the 80’s, I wasn’t even born before '98) but it somehow still made me relate and I felt every moment of the aftermath. It was just… yeah, it was a lot.
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After playing A Study in Steampunk and romancing Finch I felt any path you took towards your reunion was unbelievably bitter especially the killer route regardless of if it began with the best intentions but I also especially liked the underground resistance route since it puts you on opposing sides.
I should also add I didn’t particularly appreciate in Academy for Villains when I did everything for my mother and then she disowns me for being a teensy little monster.
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Choice of robot really got me down to some level especially when the MC made the robot so human like apart from that I don’t think any other game … 
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I really recommend Photopia in this category. It’s sort of a hybrid choice-based and parser-based game, so I say it counts.
I also remember being struck by the ending to Alter Ego, although it’s partly because it’s so sudden.
After that, things really trail off for me. End of Disc 1 of Final Fantasy VII? Lunar 2 before you realize there’s an epilogue? Story of the canner in What Remains of Edith Finch? Ending of Braid? I’m not sure what it is - most games aren’t tragic when the player’s successful, and when a game tries too hard (Final Fantasy XV), I’m more likely to react with an “oh, come on.”
Edit: I also thought of - Persona 3, especially the end (“you’re still tired”); and Valkyrie Profile, especially the beginning (“I just want to forget … forget it all …”). Both are also in my top games of all time period, if you can emulate them and like RPGs.
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For me, it was Aeris/Aerith dying to Sephiroth in FF7.
I keep wondering if Final Fantasy VII Remake will change her fate.
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I should also have mentioned Paradox Factor! Terrific sad game.
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I guess it is kind of hard to find a game that’s kind of tragic if playing successfully through it, huh. Maybe I should have worded it more like “any games that have a melancholic mood throughout the story and never really goes away”. Some examples I can think of from the top of my head would be The Grim and I and the recent Love at Elevation. Another one I can think of when the character is put under a disadvantage from the get-go or the world is already falling in ruins (either literally or metaphorically) for them would be shadows of the colossus. Most of the previous Final Fantasy games would be good too actually.
I just loved the mood throughout these games, the feeling of imperfection and longing the MC has the entire time and the ending either does little to help lift it or it’s one of those frustrating endings where all is said and done and everything is wrapped up but you don’t actually get an abysmal amount of closure
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I just found out some spoiler-stuff regarding Pathfinder: Kingmaker’s story-line that totally devastated my will to continue the pre-made characters story-arcs.
I love the game but what I found out really demotivates me from experiencing all the wonderful story-telling leading up to that point. This is material the rpg computer game makers made outside the original table-top material, so the story is deviant from the original in that respect.
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I bought and played this game just because of this thread and I’m glad I did because the story was wonderful, though it didn’t quite bring me to tears.
I think the only video game I can vividly remember crying my eyes out was the end of Bioshock Infinite and Burial at Sea one of the DLC’s.
Elizabeth deserved better 
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A Study in Steampunk gave me the experience of helplessly watching my wife die of cholera.
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The Grim and I is a very deep game. Heartfelt. I didn’t remember crying when I played through it, but it really pulled at my heartstrings. The Harbinger has a similar touch to it, but is of a entirely different plot and setting. I was moved by it, especially the ending.
I’ve been saddened by the concept withing a game, I suppose. And not the actual gameplay itself. The last wizard, for example. I find the fact that the vicious cycle of other wizards being pulled from their world into another, quite sad.
In a similar way, Avatar of the Wolf always made me feel anxious over the inevitable choice of having to either kill or be killed by the Wolf god rather dark. Because I want to do neither. There is, however, an option to skip taking the wolf’s power after defeating him. But he still dies. Can’t have both, I guess.
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Depression Quest did a number on me. I couldn’t finish it.
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Oh! That’s a little different from what I thought you were asking. You should play What Remains of Edith Finch. A woman explores her old family house and relives the moments just before each one’s death. Only 10.99 on Steam. Also available on PS4. Stumbles a little on the ending and not exactly sad, hence my less certain recommendation before, but still melancholic and super cool. (Also not quite as unflinchingly grim as it sounds - the deaths are all tasteful, sometimes more like fairy tales that you’re not sure whether to believe, and they’re sometimes darkly funny.)
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If you’re talking about cog/hog. Then there isn’t much sadness that I feel. Although Choice of Magics realy bad ending is something I’m avoiding. After getting it the first time.
Other games
Both Bioware games Mass Effect 3 and DAO. Did a number on me. Both in the right and wrong ways.
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Saaaaaaaame
#TheGrimAndI
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Creatures Such As We
I wasn’t prepared for this. Not at all.
I can’t even exactly explain why I was so sad… the feeling was just… there…
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Life is Strange broke me. In tiny little pieces, and those were broken too.
Then there’s The Last of Us. It didn’t make me sad per se but it left a sour taste in my mouth. I would’ve done the same Joel did though, even when I let Chloe die.
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