Throughout the episode "Ambush", the King of Toydaria proves to be an honorable man and reluctant to side with the Separatists. When the king finally decides for certain to to side with the Republic, Yoda saves him from assassination. To which the king is very grateful and pledges undying loyalty.
Yoda taking a moment of rest to get to know his clone troopers better, and pointing out that despite their shared appearance, they're all unique individuals.
Rex, the hard edged captain, giving the "shinies" a well done speech and saying he'd be happy to induct them into his own unit.
The ending of "Innocents of Ryloth". After the fight is over and Numa is reunited with her family, she waves goodbye to Waxer and Boil, calling them "nerra", as she had throughout the episode. When the troopers ask Obi-Wan what it means, he smiles and replies:
That entire subplot was one massive Crowning Moment of Heartwarming. Waxer's concern for Numa is adorable, as is the way Boil warms up to her in the end. This only makes what we know will happen and the revelations about Order 66 and how it works even more tragic in hindsight. The clones are mostly shown to be good people, who are going to commit a horrible act through what is essentially, programming.
In Rebels, Numa is now one of Cham's best rebel warriors. She has clone armor on one of her arms, and it has writing right underneath the shoulderplate. What does it say? Boil.
This also means that someone (if not himself) got a hold of Boil's armor and sent/brought it to Ryloth for Numa to have.
However, it seems upsetting that Numa doesn't recall Waxer.
It's a small moment, but in Liberty on Ryloth, Cdr. Ponds' first reaction to seeing how bad things are for a lot of Twi'lek villages is to see if his troops have any supplies they can spare to help.
Plo Koon treats everyone under his service with incredible respect and kindness, if a little snark here and there. He proves his Father to His Men tendencies when he's stranded with several clones in space with little hope of rescue.
Plo Koon: Sergeant, why are you so certain no one is coming?
"Bounty Hunters", Ahsoka reassuring Seripas when it's revealed that he's actually a small harmless looking alien wearing a suit to make himself more intimidating.
The ending of "Voyage of Temptation". Obi-Wan foils a hostage/assassination plot upon Duchess Satine, who he used to be romantically involved with when he was still in training. He admits to Satine that if she'd asked he'd have left the Jedi Order to be with her. Both of them acknowledge their feelings for each other, yet being unable to act on them, due to their roles in society, they part having also come to terms with their opposing standpoints on the war. After Satine remarks on what a wise Jedi Obi-Wan is, the following exchange occurs:
Satine: And yet... I'm still not sure... about the beard. Obi-Wan: Why? What's wrong with it? Satine: It hides too much of your handsome face.
The One-Shot Character Senator Kharrus from "The Gungan General". Without hesitation he gets out of his seat to assist Jar Jar, securing him safely while their ship is crashing. Sadly this act of selflessness ends up killing him. An act which genuinely moves Jar Jar himself.
Commander Stone probably says one of the nicest things anyone ever has about Jar Jar as the Gungan goes to negotiate with Hondo's men.
Clone Trooper: He's probably gonna get himself killed.
Commander Stone: Don't worry, he's smarter than he looks.
Episode 16 of third season was pretty much this. Nevermind that Ahsoka was briefly turned to Dark Side, but the beginning when Ahsoka asked if Anakin had seen a nightmare and again in the end, when after Ahsoka had been revived by The Daughter, they hugged.
Hondo telling Boba to help the Jedi:
Hondo: It is the honorable thing to do. It's what your father would have wanted.
Clone Cadet Jax sticking up for Boba during "Death Trap". Even after Boba leaves him and his fellow cadet's to die in space, Jax seems to feel sorry for him rather than angry.
Master Ima-Gun Di making his stand on Ryloth. Cut off from reinforcement, he and his men go down fighting so that the Twi'lek refugees have time to escape. The Clone Wars were always intended to serve as a corrupting force on the Jedi Order, forcing them to fight as soldiers. But Master Di shows that even amidst the war's darkness, there're still those who unwaveringly serve the light.
There's also his grave expression as he looks at his men preparing. Just like many other Jedi, he evidently doesn't see his soldiers, clones or not, as expendable. It obviously hurts him to have to order them into what is essentially a suicide mission.
Pretty much anything to do with 99.
The clone trooper Cut Lawquane from "The Deserter", who fell in love and settled down into civilian life after he'd survived a massacre.
After some friction over Rex calling Cut out as a deserter and a traitor, Rex comes to understand his choice and decides not to turn him in.
Asajj briefly seen chatting amicably with a fellow bounty hunter, despite quitting her group in a previous episode.
Anakin and Ahsoka's reunion in the end of "Wookiee Hunt".
Just a small one from earlier in the episode. Ahsoka, Chewie, Jinx, and O-Mer manage to trick the Trandoshans into an ambush. O-Mer takes control of the Trandoshan's speeder, looks over at Ahsoka, extends his hand, and, with a Casanova Wannabe-like smile, asks "Need a lift?" This boy has been in abject despair for the past two-and-a-half episodes, even more so than the other two younglings on the island. Yet, Ahsoka has got him believing in himself and his friends again, not to mention smiling again.
In the episode "Nomad Droids," C-3PO and R2-D2 are on their own on a planet with no real hope of getting back home. At one point, where things are looking particularly bleak, C-3PO quietly comments at that he'd expected to already be safe by that point because R2 was so good at getting out of these kinds of messes. It's so rare to have C-3PO actually compliment the smaller droid and it was rather nice to see.
Earlier during part one, once 3PO explains to King Manchucho that he and the clones have arrived to help. The little king gives 3PO a hug of gratitude, it's surprisingly adorable.
Savage Oppress' reaction when he finally finds Darth Maul in "Brothers". It shows that, even after all the Nightsister magic and mind control spells he was subjected to, Savage is still a caring brother. He already lost one brother last season; he didn't want to lose another.
Speaking of Savage, he even tries to go directly against Sith ideals, trying to make the case to Maul that there shouldn't be dominance between them. There's also the fact that, with Kenobi tired and drained right in front of him, Maul still chooses saving his brother over revenge. Really makes one wonder how the two could have turned out if they were picked up by the Jedi.
The way Ahsoka comforted and encouraged Prince Lee-Char through out the Mon Cala trilogy.
Jar Jar convincing Boss Lyonie to dispatch the Gungan army to help Padme and the Jedi.
Lyonie: Wesa need some thinking time to respond to disa news.
Lyonie: Yousa right. Thinking time's a done. Wesa need to be leaving now.
A subtle one (and some Fridge Brilliance) comes in the form of Anakin's slaver alias when he infiltrates the Zygerrian empire: Lars Quell. The first part of his name apparently came from his stepfather, Cliegg Lars, the man who freed his mother from slavery after buying her from Watto, showing that he thinks very fondly of him. The last part of his alias, Quell, means "to put an end to", describing Anakin's desire to end slavery like he always wanted to.
Ahsoka's conversation with Governor Roshti at the end of the episode "Escape from Kadavo".
Also, when Govner Roshti thanked the Jedi for rescueing his people, but Anakin rejected it, stating that Ahsoka was the real hero, since it was her creativity that saved the day. Ahsoka's reaction? A shy almost "ashamed" smile, and deliberately staring at the floor.
At the end of "Bounty", Ventress gets a Pet the Dog moment when she decides to free the girl who was to become a bride to the warlord and let her go with her brother.
Anakin giving Ahsoka some tips for her relationship issues in "Front Runners", a topic he's all-too familiar with.
Lux and Steela sharing a Now or Never Kiss in "Tipping Points". Ahsoka giving Lux a friendly punch on the arm afterwards also counts.
During the opening narration for "The Gathering", one of the flashbacks shown is Plo Koon taking care of a very young Ahsoka.
Petro going back to save Katooni from being trapped behind an ice wall.
In "A Necessary Bond", we have Hondo's Motivational Lie to encourage Katooni to finish her lightsaber.
Hondo: (sounding genuinely encouraging, while still being his Large Ham self) This is worth the price of a ship. To see the construction of a Jedi lightsaber, this is priceless. Finish it! And together, we can defeat Grievous...
Really, the entire episode is one for Hondo. From his almost father-like interactions with Katooni to deciding to save Ahsoka even when he's got nothing to gain and at the end, the moment where he looks back and gives a smile to Katooni before leaving, showing he's not such a bad man after all.
The latter half of "Secret Weapons", with Colonel Gascon growing fond of the droids and praising them at the end.
During "A Sunny Day in the Void", whilst he and Gascon are separated from the rest of D-Squad, WAC and the colonel hitch a ride on some flightless birds to the nearest water source. WAC proves he's not a total Jerkass when his mount nuzzles him after he pets it.
Anakin and Padme just having a (thwarted) date night at the beginning of "Senate Spy."
In "Point of No Return", when Anakin learns that R2 sacrificed himself to save everyone and was on the ship when it exploded, he immediately orders a search for him in the rubble. Listening to his tone of voice makes you realize just how much Anakin cares about the droid.
Then, when R2 is fixed, Anakin comes to see him. Just look how happy he is to see his little buddy safe and well.
Darth Maul of all people gets one when his brother is killed, briefly forgetting about the fight to rush to his side in terror.
Maul's affection for his brother is definitely unspoken rather than explicit, but in "Eminence" he looks ready to tear Pre Vizsla's throat out until Bo-Katan threatens Savage. Maul immediately backs down.
Anakin in "The Jedi Who Knew Too Much". He refuses to believe Ahsoka could be a murderer, and does his very best to try to convince her to come back peacefully. From the same, Rex is also quick to deny Ahsoka being a killer.
In the final scene of "The Wrong Jedi", Ahsoka leaves the Jedi Order, and Anakin runs after her to talk to her. The conversation is a mix of tear jerker and heartwarming. He empathizes with her and her desire to leave, and Ahsoka replies that she knows he feels the same way. Regardless of how much of a tear jerker it is, it ends heartwarmingly as Anakin lets her walk away and watches her proudly.
The episode has a smaller one for Obi-Wan, who is the only one on the Council who remains vehemently opposed to giving Ahsoka up to the Senate. He even moves to follow Anakin as he runs after her when she leaves, though Plo steps in so Anakin can have a moment alone with her.
According to interviews with Filoni, as well as Plo's disbelief in the accusations levied against Ahsoka (even when presented the false evidence), Plo probably voted with Obi-Wan, even if he didn't get to say as much and hides his emotions better. Given their close relationship, it would be harder to believe he went along with the majority opinion.
Even though the Council made some massive errors in judgement, they should at least get credit for recognizing just how badly they screwed up. Their conversation with Ahsoka can essentially be summed up as "You put up with way more crap than you ever should have, and we're going to knight you for handling it as well as you did."
Even Ventress gets one, genuinely sympathizing with Ahsoka's plight and calling out Anakin while she's at his mercy for both him and the Council abandoning her. This is actually what gets Anakin to hear her out calmly.
"The nightmares...are finally over." Also doubles as a Tear Jerker.
Obi-Wan trying to relate to Anakin about what he is going through with Padme, showing that while he does not fully grasp at Anakin relationship with Padme, he still wants to help. (Also a bit of fridge brilliance since it can also be seen as a nod to ROTS)
In Yoda's season 6 arc, there's a brief moment where Obi-Wan takes a jab at the council's lax judgement as of late, clearly meant to remind them of the debacle with Ahsoka. Given Yoda's vision of Ahsoka in that same context, it obviously hit home.
The unerring faith and reverence the rest of the Jedi Council holds for Yoda during his arc. The scene where they meditate with him simultaneously is a highly notable moment.
While the idea that Jar-Jar has a girlfriend in the form of Queen Julia is a Crowning Moment of Funny in itself, you must admit his attempts to save her and her belief in him is this.
The way Mace Windu's attitude towards Jar-Jar changes over the course of "The Disappeared" two-episode arc. At the beginning of the story, Mace's typical reaction towards Jar-Jar is that of annoyance. Then he begins to grudgingly respect the gungun. At the end, it's clear that Mace has come to view Jar-Jar as a friend. Considering that The Clone Wars softened many people's opinion of Jar-Jar, Mace Windu could almost be considered an Audience Surrogate.
A subtle one from "Orders", but the idea that the clones have their own bar on Coruscant, and there's no "separate but equal" clause being enforced here as even non-clones are allowed if you look carefully. This alone suggests that the Jedi Order was already working on getting the clone army more civil rights despite their status as technical slave soldiers, and had the war ended in their favor, they would have tried to get them away from the Kaminoan government and integrate them into society. Also a Tear Jerker as well when you consider how the war ultimately ends and, according to interviews with Filoni on Rebels, the clones didn't get any compensation and a lot of them are still serving as slaves despite being old men and deemed no longer fit for combat, only this time under a tyrannical regime.
In a strange way, in Son of Dathomir, Maul is actually rather benevolent (in comparison to, say, Grievous or Vizsla) to the Super-Commandos and trusts that their loyalty is genuine and can get the job done.
Likewise, Kast and Saxon (as well as the other Super-Commandos) show concern for his health and being when they rescue him from Stygeon Prime and their loss at Zanbar.
Kast: Lord Maul - I was afraid we'd lost you.
Maul: Take us away from here, Kast... I can no longer stomach the sight of [our loss].
The "Bad Batch", a team of mutant clones who nonetheless have desirable traits, are known as "Clone Force 99". Given how 99 was considered a defective clone, that this group would have their group named for him is kind of sweet. Even Rex realizes where they got that number (even though it isn't explicitly mentioned).
Gets a little twisted when in the NEU's Marvel's Star Wars comic series, there's a Stormtrooper task force called Task Force 99, under a government that has perverted every ideal the clones believed they would win the fight for.
"Wookiee Hunt": Even though Chewbacca was credited as "Himself", special mention was given in the credits to Peter Mayhew for being "the heart and soul of Chewbacca".
"Secret Weapons": The pink astromech being named QT-KT, "KT" as in the late Katie Johnson, daughter of 501st (the real life costuming group) founder Albin Johnson who died of brain cancer, and had a pink astromech droid built for her.
The Return of Ahsoka in Disney's new show Star Wars Rebels after their complete takeover of the franchise. Heartwarming enough just to show that she not only survived Order 66, but is also one of the creators of the Rebel Alliance. On a more Meta level it also shows that Disney does care about the fans of the old shows and continuity, since only they would know or care about the character.
Repeating what happened above, the trailer for Star Wars Rebels Season 2 reveals that not only are Clone Captain Rex, Commander Wolffe, Commando Gregor and pirate captain Hondo Ohnaka returning, they are allies to the Ghost crew and the Rebellion. As a bonus for the clones, them serving the Rebellion means that not only could some other clones have refused to follow Order 66 and/or fight for the Rebellion (in spite of the microchips implanted to brainwash them, though if you look closely, you'll note some scars in the area where the chip would be under), Fives' investigation of the Order 66 conspiracy and his death weren't in vain after all.
The fortune cookie at the beginning of "The Bad Batch':