In The Smurfs and the Book that Tells Everything, Brainy obtained the attention and respect he always wanted, using the aforementioned book to give the other Smurfs easy solutions for all their problems (even though in the end they end up having nasty side effects). When the village is flooded, Brainy finds himself stranded on a rock in the middle of the swelling river with the book and Baby Smurf; unable to swim while carrying both, he asks the book what to do. The book tells him to abandon Baby Smurf to drown, as the book itself is more important than him. Brainy, after a brief Stunned Silence, calls the book a monster and throws it in the river, before swimming to safety with Baby. Even if Brainy can be an insufferable know-it-all, and may cause a lot of trouble, he didn't even think about doing what the book said.
"Once in a Blue Moon," when Baby Smurf enters the village. He even gets the usually grouchy Grouchy Smurf to warm up to him, even to a point acting as Baby's guardian when the threat of Baby having to return from when he came arises. It allows Grouchy to show a softer side and develop some of his character.
That episode "The Dark-Ness Monster", where Brainy loses his glasses and has to rely on Clumsy to lead him around. Actually, Clumsy tends to instigate these by his mere presence.
The episode "The Smurfiest of Friends" shows just HOW much Clumsy likes Brainy as a friend - he's the only one who wants Brainy to attend the party thrown in his honor (and this is AFTER Brainy ended their friendship); he immediately goes looking for Brainy once the Smurf disappears; when he does find Brainy, he's perfectly willing to take his place as a prisoner if it means Brainy can get away, and as they both head back to the village, he tells Brainy that he would rather be with him than his friends and that he loves him. This makes Brainy so surprised that the least he can say to that is "I know just how you feel".
"Hefty's Heart" Hefty overcomes the yellow hate disease, something that shouldn't even be possible to resist, because he naturally has so much love in his heart. The 1st half of the episode showed exactly how nice and helpful Hefty normally was around the village, and it's sweet to see him ultimately put aside hateful feelings and rescue his friends.
"Fire-Fighting Smurfs". Most of the episode also crosses over into Tear Jerker territory, but it ends on a very happy note. Snappy is forgiven for his mistake, he takes responsibility by taking care of the animals and planting new seeds to replace the old trees, and he's awarded with a medal AND the animals nuzzling him in thanks.
Heartwarming moments outside of the comics and cartoon series:
Papa and Patrick's talk on the apartment roof about being a good father.
Every time Grace holds Clumsy in her hands, it's just so ridiculously adorable.
There's also something sweet about Grace's bonding moments with Smurfette; considering that Smurfette's never had a female figure in her life, it's touching to see Grace immediately settle into a kind of 'big sister' role to Smurfette.
From the deleted scenes, Papa Smurf's lullaby. It's just so sweet and heartwarming.