"Naughty Nautical Neighbors". After Squidward sabotages SpongeBob and Patrick's friendship, the two then try to make HIM their new best friend, resulting in all sorts of chaos. Squidward finally decides to get them back together, so he stages a dinner between them and it turns into a competition between SpongeBob and Patrick to see who can get more soda from Squidward. Naturally, Squidward soon runs out of soda, so he tells the two to sit tight and leaves to get more. By this point, SpongeBob and Patrick have become inflated with the soda bubbles and hiccup some out. They become so amused with this that their friendship is renewed, much to Squidward's relief—-and horror, for the bubbles destroyed his house.
Squidward: He sure did. Ate the whole thing in one bite.
SpongeBob: *stops crying* No drink?
Squidward: Nah. Now take me home.
"Home Sweet Pineapple". Nematodes destroy SpongeBob's house, rendering him homeless. In order to avoid leaving Bikini Bottom and moving back in with his parents, SpongeBob and Patrick try to make him a new home. All attempts fail miserably. Having no choice, SpongeBob first takes a pebble (the only remnant of SpongeBob's destroyed home) and buries it. He sheds a tear on it, and prepares to leave. Squidward, happy that SpongeBob is leaving, starts dancing on where SpongeBob's house used to be. However, we soon learn that the pebble was actually a seed, and the tear SpongeBob shed provided its water, allowing it to grow into a new pineapple and eliminating SpongeBob's need to leave. On top of Squidward .
In "Culture Shock", Squidward mentions to Mr Krabs that the talent show would bring in a lot of money, as well as make Pearl a star. Mr Krabs, who, as we all know, is obsessed with money, is more happy at the idea of his daughter becoming a star.
In "Texas", the Texas-themed party that SpongeBob and Patrick arrange for Sandy after hearing her pine for her home.
Basically any time Mr Krabs is nice to Spongebob in season 1. Starting in season 2, Mr Krabs became more callous and mean-spirited. Because of this, it's rather sweet to watch an episode like Squeaky Boots, where he's trying to comfort a crying Spongebob after the little yellow guy "lost" the boots, or Suds, where Mr Krabs is actually concerned about Spongebob when he's sick, and sends him home to get some rest. (In later seasons he really doesn't seem to care for the well-being of his employees.)
"Christmas Who?" Especially when Squidward dresses up as Santa and gives out his stuff to appease the people of Bikini Bottom.
Also when Squidward begins to feel bad when SpongeBob gets depressed because he "ruined" Christmas.
At the end of the episode, where SpongeBob gives Squidward a handmade wooden clarinet.
"Thank you, Santa...for bringing Christmas to Bikini Bottom!" "I didn't bring Christmas to Bikini Bottom, SpongeBob. You did." Keep in mind that this is Squidward saying this.
"Band Geeks". You know what scene we're talking about.
There's a reason this episode is universally regarded as one of the best episodes made.
In "Grandma's Kisses," after SpongeBob's temper tantrum, his grandmother tells him that he doesn't need to be a baby to get his grandma's love, and that no matter how old he is, he will always be her baby boy. It's a sweet moment, even if it's somewhat downplayed by Squidward and the Krusty Krab customers laughing at them through the window at the end.
Squidward is very caring for Spongebob in "Graveyard Shift", and when he thinks he's going to die, he says he's always been OK with him. Then Spongebob goes off topic.
"Mermaidman and Barnacleboy V". Barnacle Boy gets fed up with how Mermaid Man treats him like a sidekick and decides to join Man Ray and the Dirty Bubble, and form EVIL. Later on, Mermaid Man asks SpongeBob, Sandy, Patrick, and Squidward to help him save the world and defeat EVIL, by putting on the costumes of the original IJLSA, and in the process, gaineachcostume'ssuperpowers. The two sides engage battle with EVIL, who end up winning. The ending (and the heartwarming) starts when Barnacle Boy confronts Mermaid Man, and demands three things: one, to be treated like a superhero and not a sidekick; two, to be called Barnacle Man; and three, to get an adult-sized Krabby Patty. The demands being used to make amends is enough, but the clincher comes in the next scene:
Mermaid Man: Good to have you back on the side of justice, Kyle. Let's go get you that Krabby Patty.
At the end of "The Great Snail Race", Patrick's pet rock somehow wins the race. In a surprising display of thoughtfulness, Patrick has the trophy engraved to Squidward instead, knowing how much he wanted to win. Squidward is genuinely touched. The fact that this time, Squidward actually just laughed it off after his name was misspelled on the engraving makes it better.
The entire ending of that episode; first, Spongebob has a Heel Realization when Gary gets severely injured on the track and apologizes to him tearfully. Then, Snellie gives up the race to help Gary. And finally, when Rocky wins, Patrick is so happy that he laughs until he cries.
The fact that Patrick, in contrast with Squidward and Spongebob, is happy to let Rocky go when he feels like it rather than telling him to win.
The part when SpongeBob and Patrick are dying from dehydration under a lamp, lamenting that they never got to Shell City, or retrieved King Neptune's crown. Suddenly, they see a sign that reads "Shell City" and see the crown not too far away from them. Overjoyed that they actually reached Shell City, they begin to sing their favorite song, "I'm a Goofy Goober", until they dry up completely. The cinema-going pirates are by now in bits. However, a single tear made up of two they each shed trickles down the wire, short-circuiting the lamp's socket. This creates a puff of smoke that sets of the water systems and revives them. This triggers tumultuous applause from the entire audience. What makes the scene even more effective is that SpongeBob and Patrick have all along been trying to prove they were men, not kids. However, if they hadn't been so emotional, they would've died.
Gary and SpongeBob's reunion at the end of "Have You Seen This Snail?"
The ending of "Best Frenemies". Especially after seeing Mr. Krabs and Plankton's past in season five's "Friend or Foe".
The second-to-last scene in "New Leaf" where Mr. Krabs and Plankton spend the day at a carnival, even though the final scene turned out to be a trick Plankton pulled throughout the whole episode.
Brief moment, but in Krusty Towers, Squidward genuinely doesn't seem to mind letting Spongebob and Patrick share his pool. Considering his normal nature, that's pretty surprising.
The song from "Truth or Square" about the Krusty Krab.
Mr. Krabs' grandfather still loving him despite the fact he lied about being a pirate in "Grandpappy the Pirate".
"Porous Pockets" has SpongeBob gain an enormous amount of cash, and shares it generously with his friends and complete strangers (who blatantly milk it). Patrick, for once gaining the Smart Ball, attempts to warn him he'll lose everything at this rate, though by this time SpongeBob has let the popularity go to his head and ignores him. When the money (and as a result his new "friends") inevitably vanishes, Patrick near instantly forgives him and lets him play with his new volleyball (in fact a huge diamond).
Spongebob and Patrick making it up to their titular neighbor in "Giant Squidward" by making him a giant clarinet, showing how bad they feel sometimes for pestering him. Shame it doesn't last long.
"Kracked Krabs". After Mr. Krabs loses the cheapest crab award, SpongeBob helps him get it back and they both show semblances of their old personalities. They lose it again but they don't care because they still love each other.
In "Enchanted Tiki Dreams", SpongeBob and Patrick have one of those moments where they realize how miserable they've made Squidward and vow to make it up to him. They spend the entire night creating a paradise for him and making sure he has a wonderful time. Then, even after it all falls apart, they help him continue to relax. After all the crap he has been put through as the series goes on, it is nice to see him actually WIN for a change.
SpongeBob saving Gary from Mr. Krabs in "The Scent of Money." After seeing SpongeBob as a Yes-Man to Mr. Krabs, who got worse and worse each season, this is refreshing to weary fans. It also redeems him for his shocking behavior towards Gary in "A Pal for Gary."
The end of "Love That Squid", where Squidward, after being designated to being a luckless Chew Toy for the bulk of the show, outright succeeds in getting a date with a girl. If that isn't the writers deciding to give Squidward a Pet the Dog moment, who knows what is?
As awful as "A Pal For Gary" is, it does have one moment of heartwarming: when Spongebob is nearly eaten by Puffy Fluffy, Gary's first response is to immediately come to his rescue, even after all the crap Spongebob put him through during the episode. Now THAT'SUndying Loyalty.
The end of "Free Samples" with Mr. Krabs letting SpongeBob make money angels with him in the big pile of money. Made more nice when you consider how Mr. Krabs acted in the past few seasons.
Karen forgiving Plankton at the end of "Karen 2.0". After the fight, Karen loses all of her power and is deactivated - and Plankton, instead of going for the formula, removes the battery from Karen 2 and uses it to restore his wife. If that doesn't prove he loves his wife, nothing does.
In "Treats!" SpongeBob sleeps next to the pet store to get a can of Gary's beloved Snail Bites as soon as they open. Then, when it turns that they're all out, he goes on a world-wide search for the last few cans of Snail Bites just so Gary can be happy. After watching the infamous "A Pal for Gary", it's refreshing to see their loving relationship restored.
In the season finale, "Hello Bikini Bottom": the "Giving Up" duet between SpongeBob and Squidward, where SpongeBob tells Squidward that they can be successful on tour and Squidward seems to like him. The Bikini Bottomites who hear it end up loving it.
In a meta example, this was Aaron Springer's final episode before he moved on to Gravity Falls. Springer had a turbulent career in Season 5-7, but he also wrote greats like Band Geeks and more recently Treats!. Once you realize that he had been with SpongeBob since Season 1 (13 years) and this heartwarming episode is his finale, it qualifies as a Tear Jerker.
Plankton getting a happy ending with his new pet amoeba Spot in "Plankton's Pet". After all the failure he went through, it seems that even Plankton deserves a special reward.
SQUIDWARD of all people saving Spongebob and even admitting to him how much the Krusty Krabs needs him in Spongebob, You're Fired!After everything he's put him through, too! Squidward, dude, you've won me back my heart.
Also, Gary getting slightly un-Flanderized, and caring for Spongebob.
Not In The Show Itself
The end of the song "Where's Gary" (on the Best Day Ever album) [[spoilers: in which Spongebob and Gary are reunited]] in the end.
Several evangelical Christian groups in America criticised the show for advocating homosexuality after a video featuring SpongeBob was supported by the We Are Family Foundation (coincidence), who supports gay rights. Although Stephen J. Hillenburg said SpongeBob was asexual, John H. Thomas, the United Church of Christ's general minister and president, said the United Church would welcome SpongeBob into their ministry:
"Jesus didn't turn people away. Neither do we."
Ernest Borgnine, who has voiced Mermaid Man since season one, passed away in 2012. What did Nick do? They ran a completely un-advertised Mermaid Man marathon, with every episode from the original "Mermaid Man" to the final "Mermaid Man Begins", in his honor.