Examples for Wakko's Wish have their own page.
The Warners' segments
The ending to "Clown And Out," where, after all the abuse the Jerry Lewis-sounding clown gets throughout the short, he finally finds an audience who won't hurt him — a group of juvenile Martians.
Clown: I like it here! 8D
Also, earlier in the episode, the Warners are having a blast celebrating their brother's birthday, even though they are only three of them there.
Plotz doing an uncharacteristically nice deed by hiring the clown to surprise Wakko for his birthday, in spite of being extremely frightened of clowns himself. It goes unrecognized due to Wakko's even greater colurophobia, but that's big coming from Plotz.
There's a scene from "Temporary Insanity", before Yakko is thrown out of Plotz's office, where Wakko is making a silly face and Dot is laughing as she watches him. They're bonding.
The last of the "Animator's Alley" segments ends with the Warners saying good night to each other.
Yakko: 'Night, Wakko.
Wakko: Goodnight, Dot.
Dot: Goodnight, Yakko.
For a brief moment earlier in those segments, Dot is enjoying having a water gun fight with Wakko.
The song "There's Only One of You". It's corny, but it manages to warm a few hearts.
Don't forget It's New Year's Eve, complete with kissing and hugging.
"Little Drummer Warners," a whole episode that's a recitation of slightly-edited versions of "We Three Kings" and "Little Drummer Boy." It shows the Wise Men and the Warner Brother (and Sister) Shepherds visiting the baby Jesus, with the latter giving a loud but earnestly cheerful and appreciated show.
Warner Siblings: And he smiled at me, ba-rum-bum-bum-bum... me and my drum.
Right after the middle and right before the ending of I'm Mad, when they start getting along.
Scratchinsniff being nice enough to take the Warners to an amusment park and keep them from fighting each other is refreshing to see considering how frustrated he normally is when around them.
Hell, any time they show the quasi-paternal relationship between the Warners and the doctor, since he's the closest they have to a guardian.
"Because we love you!" from Taming of the Screwy.
The Warners really get along in Garage Sale of the Century.
"Super Strong Warner Siblings"
Yakko: Here, have a bag of money.
The "Variety Speak" song segment ends with Yakko hugging Wakko and Dot and all three grinning at the camera.
Dot and Yakko deliberately losing at checkers with Death just so they can be with Wakko.
At the end of One Flew Over the Cuckoo Clock, Skippy's lack of presence snaps Slappy back to being her normal crazy self instead of just plain crazy. She then proceeds to escape the nursing home in Cool Old Lady fashion in order to find Skippy. When the viewer sees Skippy, they get this:
Skippy: Starlight, star bright, first star I see tonight... (sniff) I wish I may, I wish I might, have the wish I wish tonight...I wish Aunt Slappy would get better and things were like they used to be...
Slappy: (opens door) "Hey, Pinnochio...I ain't the Blue Fairy, but I think your wish just got answered!
Skippy: Aunt Slappy!
Slappy: Come on, kiddo. Let's go home.
Skippy: Alright! (they embrace each other, and then the scene cuts away to them dancing into the sunset)
"Bumbie's Mom". Slappy takes Skippy on a plane ride all the way to the isolated home of the actress who played Bumbie's Mom (but hasn't for at least 40 years), just so Skippy could stop being so heart-broken over seeing a death in a movie they saw.
No Time for Love. Who knew a cuckoo clock falling in love with a canary could be so tragic and heartwarming?