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.
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.
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.
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.