Foster's Home for Imaginary Friends movie, "Destination Imagination": After the climax, Frankie wants to free the antagonist, a Reality Warper with serious separation issues who'd destroy any would-be rescuers so long as Frankie stayed by his side. Mac, Bloo and the gang, who have just narrowly escaped his giant monster form, try to talk her out of it. Herriman, who has been absolutely brutal to Frankie (even moreso in this movie than throughout the rest of the series), tells her, "Miss Frances, I have known you since you were a young child. As I have watched you grow, I've been amazed at your lack of maturity, laziness, and lack of judgement. And I realize...I was wrong." He goes on to say that if Frankie wants to set him free, he trusts her judgement. Later, when the villain-turned-good-kid tells Herriman Frankie is a wonderful person, Herriman lays his hand on her shoulder and agrees, "That she is." It's not as touching if you don't know the characters as well, but to any long-time fan of the series...Ocular Gushersto the max.
Not to mention Frankie sewing a body just for World so he doesn't have to jump around at everything all the time, and that the toy chest sort of becomes a playground for everyone at Foster's - with Herriman and Frankie shown to gleefully jump in too. It's wonderful.
The ending of the episode Go Goo Go qualifies too. DI's just still happens to top it. But in case you're wondering how the ending of the former goes, Mac comes into the room where Goo is crying, asking if Goo is okay. It turns out that Goo felt lonely and that's why she created all the IFs. Mac gave her a speech about how imaginary friends are real friends and if she got to know the ones she already had then it would likely alleviate her feelings of loneliness. Mac, not realizing that the speech had cheered up Goo enough that she's already smiling, then apologizes for his Minor Insult Meltdown (the cause of her crying in the first place) and tells Goo that he wants to be friends with her—which causes an excited Goo to hug Mac. In the aftermath, Goo is finding homes for the IFs and has become the friend of the month as a result, while Mac has joined in on her wackiness.
Herriman's 'Funny Bunny' routine, though funny and at times cringewarming saccharine, is made really heartwarming by the fact that this is Mr. Herriman we're talking about. He's still Madame Foster's imaginary friend even after all those years. Awww.
The ending of "Bye Bye Nerdy".
Good Wilt Hunting TO THE MAX.
The Sweet Stench of Sucess, Bloo becomes a celebrity, but can't see his creator, Mac, which leaves Mac heartbroken. By the end of the episode, they meet up again, and even a Jerk Ass like Bloo admits that he loves (no, not THAT kind) Mac more than anything.
No mention of "Who Let The Dogs In?" That moment near the end, before the happy twist, where Frankie gently takes the last puppy from Eduardo, sadly saying just "I'm sorry, Ed..." - and then Eduardo QUIETLY COVERING HIS EYES AS HIS SHOULDERS SAG...well, it takes a stronger man than This Troper not to find themselves on the verge of Manly Tears.
Even though it was intended to be a funny moment, the book end of the series was one for this troper. The opening animation shows the house being drawn, and the closing animation of the episode "Good-bye To Bloo" shows the house being un-drawn, as if to say "Thanks for watching, but all good things must come to an end." Followed by a thanks from Craig McCracken and Lauren Faust in the closing credits.
I guess it depends on how you see it, because that had me crying for a few days about my childhood dying with the show's end.
In "The Big Picture," Camery laments about not being able to be a part of the yearly Foster's Home photo because he's the one taking the photo. At the end of the episode, Herriman has a mirror-friend stand directly across from him, so he is in the photo.
In "Busted," Bloo was under the threat of expulsion from the house from Herriman if he kept breaking the rules. After accidentally breaking Madam Foster's bust (Get you head out of the gutter!), Wilt offers to take the fall for Bloo, which he politely refuses. Considering that this was after Bloo's Flanderization started, you'd expect him to jump at Wilt's offer.
Although not heartwarming in the usual sense, the times throughout the series where Herriman and Frankie got along and worked together.