Ever17 has several moments, but the most heartbreaking bit is the Luke, You Are My Father moment from Kid, when he and Sara confront unrepentant Jerkass Tsugumi and force her to admit that she's their mother. She wavers for a minute or before finally breaking down into tears, begging forgiveness for abandoning them and hugging both tight as they run to embrace her.
The whole part describing what Tsugumi went through after escaping from Le MU at the expense of Takeshi's life, how she almost gave up on living because the love of her life was dead, ran from Leiblich, lived as a homeless person, found out she was pregnant, regained hope in life because of her children....just everything about that.
On the Tsugumi route. Hot damn, that was a really, really depressing Heroic Sacrifice...
The ending of "After You've Gone", the Drama CD. Tsugumi breaking down into tears and embracing Sara after the latter recovers from the fatal virus always touches this troper's heart.
In the Xbox 360 remake, mixed with a Crowning Moment of Heartwarming, the reunion with Takeshi and Coco. In the original, only Hokuto went down to see him, and he had spoken to both of them before. In the remake, everyone goes down to IBF to see them wake up. Hokuto and Sara happily welcoming their father back as he woke up (this being both their first meeting with him, as Hokuto hadn't spoken directly to Takeshi in this version), and Tsugumi seeing him for the first time in 17 years, only to tearfully berate him for leaving her alone for so long.
And, related to all the previous examples, Karma. Not only when you hear Karma playing, you know you are in for a Bad Ending or another kind of heartrending scene, but the song is a Tear Jerker by itself. Just listen to it