Heartwarming: Nine Hours, Nine Persons, Nine Doors
After getting every bad ending before going for the True ending path, finally reuniting Snake and Clover. The other paths screwed them over entirely. Clover either snapped because she thought the other players had murdered her brother, or she was murdered herself, never finding out that her brother was still alive. For Snake, he ends up trapped in the chapel's coffin, and without the code to the coffin's lock, it's very likely that he dies there. In the Safe ending, he's rescued, but his sister is killed, and he sacrifices himself to make sure the killer is punished for it. Having it all come together through all of the depressing alternate routes made it all the more heartwarming.
Junpei and Clover share a sweet scene when he gives her the laminated four-leaf clover and tells her the following:
No matter what happens, you can never lose hope. You have to remember what's most important, and that's to have faith, and to have love. If you can remember all of those, that'll bring you good luck.
This gets a Meaningful Echo when you're on route in figuring out what is really going on and Clover, instead of going Ax-Crazy, tells Junpei those words are what kept her from giving into her anger and paranoia. That whole scene is quite touching, actually, especially when Clover glomps Junpei when she realizes the body behind Door 3 isn't her brother. Chances are you won't be seeing this scene until you sat through some of the bad routes which involve a perpetually depressed and apathetic Clover, so to finally see something go right for this girl is quite sweet.
In the true ending, Seeing Akane and Aoi hug after she escapes the incinerator.
In the true ending, Clover and Snake reunite after the coffin opens. Junpei and Seven of course have to remind them that time is of the essence, but they can't bring themselves to.
Also in the True Ending, Seven offers to stay behind in the Chapel so two teams of 3 could leave. Later, Lotus offers to stay in the incinerator so that Junpei, Snake, Clover, and Seven can escape. Both instances are refused by the others. In both cases, they act like the others are making a mistake, but Junpei notes that their eyes are wet.
More on the true ending...the way Santa seems to describe himself as Santa Claus "making a wish come true" while hauling Ace out the door, combined with his story of how he used play Santa for Akane/June makes it feel like he was delivering one final present for her: The end of the career of the monster which destroyed her life (and by writer account, turned her into a fairly cold and calculated person)
The scene where Junpei, Santa, Lotus and June (or Junpei, Snake, and Seven) meets up with the rest in a room next to the staircase gate.
They were happy to simply see one another again. Although the level of cheer varied greatly from person to person, each one of them was wearing some manner of smile. Almost as though they had forgotten the death of the 9th man... No, thought Junpei, perhaps that wasn't it. Perhaps the thoughts of his death was what drove them to smile at one another. Not in a morbid or hateful way, no. The 9th man had died, but they were still alive, and that was something to be happy about. A sort of simple, uncomplicated joy, Junpei thought. The joy of being alive.
This is extra heartwarming/tear jerking when you realize that the third person perspective in this scene is actually from Akane's point of view. She appreciates the joy of being alive because she's struggling desperately to survive.
The epilogue. After experiencing all the horror of the Nonary Game, most of the characters are free from all danger and just joking together on a road trip. Running parallel to this, the scene with young Junpei and Akane on the hilltop is both heartwarming and a Tear Jerkerbecause it's probably one of the last times they ever saw each other before Akane was kidnapped.
A meta example: As part of 'Operation Bluebird', fans were asked to express what they loved about the series. Unsurprisingly, many of the answers were so heartfelt as to qualify for this trope.