Crocker: (Hugs Poof, eyes start to water) Be strong (Lets go)..n-no tears....(Breaks down sobbing).
In "Boy Toy", when Timmy realizes the absolute hell that Tootie lives with Vicky every single day, realizing he's getting off easy. This on top of his remorse for his absolutely cruel treatment of her (because of her Stalker with a Crush tendencies) convinces him to Pet the Dog.
The ending of “The Secret Origin Of Denzel Crocker”, where, despite all of Timmy’s efforts to fix Crocker’s past, he ends up becoming the cause of all his misery by accidentally revealing his fairies to the world. The worst part is that Timmy wasn’t doing it for any selfish intentions, he genuinely wanted to help Crocker to not be so miserable.
’’’Young Crocker:’’’ NO! Do you realize what you’ve done? DO YOU!?
’’’Timmy:’’’ No! I’m sorry! This is exactly what I was trying to prevent!
In "Fairy Idol", the moment where Timmy finds out that Cosmo and Wanda can't be his fairies anymore, even if they accepted his apology, the only thing they can do is walk him home. They get better, but its still a sad moment.
Timmy: Can we take the long way home?
In the same episode, when Timmy thinks Cosmo and Wanda are dead. They get better, but still.
Just Fairy Idol in general. Even if it does have some funny moments, it's probably the most depressing Fairly Odd Parents special ever.
During the Magical Duel between Timmy and Remy, Timmy tries to convince Remy to call it off, saying that he doesn't care that Remy has a Fairy Godparent. Remy's response is just heartbreaking.
Older!Timmy crying about wanting to get out of jail and see his parents in "The Big Problem!". Fortunately, this brings out the kid in him, allowing Cosmo and Wanda to change him back.
Cosmo and Wanda's "With You" number from "School's Out!" is so emotional. The song is about how despite Cosmo's naive nature, they still love each other and will stick together even in the toughest of situations. Even Jorgenhimselfwas incredibly moved.
"Where Is The Fun", a chorus between Timmy, Flappy Bob and the Pixies, in which Timmy tries to get Flappy to see what's really going on while the Pixies try to drive him further into villainy. Poor Flappy can't decide which side he should go to... but in the end he picks the Pixies' side.
Flappy Bob:Maybe you're right / Could be a giant mistake / But changing my life's a risk I'm not ready to take / This nose, pants, hair and shoes / They're all my past and now I choose / To wish for a world / A world that fits all my views / A world where I'm safe!
At one point in the song, Timmy asks Flappy how he thinks his parents would feel if they discovered what he's become. Flappy promptly looks at a photo of his parents and startsto cry.
The look on Chester's and A.J.'s faces at the end of Wishology Part 2 when Timmy sacrifices himself to the Darkness. Even though, it's Limited Animation, the expressions on the boys' faces when they realize they may never see their best friend againis truly heartbreaking; and they didn't have to say a word. Hell, even Vicky and Trixie are shocked at the fact they may never see him again.
Timmy revealing Cosmo and Wanda's existence to his parents in "Abra-Catastrophe!" to save them from being used by Crocker.
Cosmo: But we don't wanna go away forever!
Wanda: We love you!
Timmy: I love you too. And that's why I had to do it, because... THE TRUTH WILL SET YOU FREE!
At the end of Meet The Oddparents, Jorgen finds out that Timmy's parents know about his fairies and, as per Da Rules, says he has to take them away forever. Cosmo, Wanda, and Poof tearfully beg Jorgen not to do it, and while Timmy tries to insist he'll be fine and that it was worth giving his parents the time of their lives, it doesn't take long before he too breaks down crying and hugs them while saying how much he'll miss them.
Meta example: The death of Adam West, Catman's original voice actor.
When Timmy is revealed to have wished for Comic-Book Time so that he'd never lose Cosmo and Wanda, Jorgen fixes the wish. This turns Timmy into an adult, ended all of his wishes. Not only does that include Poof, but he must erase Cosmo and Wanda's memory of their son. This is so traumatic for Jorgen it causes him to become morbidly obese to deal with the stress.
In Fancy Schmancy, Chloe sings a sad song that she and Timmy cannot spend their three-month best friend anniversary because of their parents.