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Tear Jerker: Shrek Forever After
At the end, there's an extended amount of time where it appears that Shrek failed. And, technically speaking, he was dead for a while. This movie being Darker and Edgier than the others, it wasn't unbelievable that they'd do it.
There's also the moment somewhere right after he's beginning to understand what his impulsive wish did - he finds his daughter's doll still in his back pocket from where he'd put it very early on in the film, and the look on his face as he realizes that she doesn't exist anymore is absolutely heartbreaking.
The song "Fiona Doesn't Love Me" and the accompanying scene. Shrek thinks all he has to do to break the spell is get Fiona to kiss him, par the rules of True Love's Kiss. He manages this, but because she doesn't know him that well and thus doesn't love him, nothing happens. Donkey asks him what went wrong, and he has the most despairing look on his face as he says, "But Fiona doesn't love me."