"Don't ever apologize for being extraordinary, Anakin."
Nobody could rile him [Anakin] up as much as Obi-Wan Kenobi. And no one could make him feel so honored to be called a friend.
Also, Anakin beaming with pride at Ahsoka in the beginning of Siege when he discovers she rescued Obi-Wan and the clones.
Legacy of the Force: The two heart-to-heart scenes between Ben and Mara in Sacrifice, which demonstrate why Mara is such a Mama Bear (scared of losing her closest family, the two who gave her renewed faith in life).
Mara: "Ben, you're probably going to see a side of me soon that isn't good old Mom. But I want you to know that whatever I do, however much of a stranger you think I become, I love you, and you're my heart, every fiber of it. Nothing matters to me more than you."
In the X-Wing Series, after Dia shoots Castin and undergoes a Heroic BSoD, Face takes her in his arms and keeps her from killing herself. Later he asks about the last time she really enjoyed herself, and then the last time she felt safe in someone else's company.
Dia: "It was when I was at my worst. When I had shot Castin, when I'd desecrated the corpse of a brave man and pretended to do it with glee. When I tried to kill myself and you would not let me. Just before I fell asleep, I knew that you would not let anyone hurt me. You would not even let me hurt myself. And in that moment I knew myself safe, for the first time since I was a child. [...] That's what I wanted to say to you, what I didn't know how to say before. That I know you feel you failed Ton Phanan. But you did not fail me."
How Mara Jade gets Luke to say "I love you": when he puts her in a Jedi trance, she tells him to wake her with that phrase, while wondering if he could actually do it. This is in Vision of the Future, and comes right after a now or never moment.
Going along with the previous example, the birth of Ben Skywalker later on in the same book.
The biggest Heartwarming (also a Moment of Awesome) in that book and perhaps the entire New Jedi Order series would have to be Jacen channeling his father's Big Damn Heroes moment in the very first movie. Jacen, still in his straw pacifist stage, has threatened to leave the Falcon because he doesn't want to participate in his father's raids on collaborators' ships. Leia visits Jacen, telling him that Han still needs him, and is desperately afraid of losing his bond with Jacen because Jacen is a Jedi, dealing with so many things Han could never understand. This is how it breaks down:
Jacen: This is one of the hardest things I've ever had to do. Leia: You're still going? Jacen: I decided to stay with you guys two days ago.
Commander Thrawn telling Jorj Car'das not to tell Ferasiwhat he did to Outbound Flight, because there are too few true, honest idealists in the galaxy and he wouldn't want to be responsible for crushing even one of them. Followed by Thrawn using Car'das's first name for the first time. You'd think that causing the deaths of fifty thousand innocents would have put Thrawn well over the Moral Event Horizon, but—well, that was not his intention, and if C'baoth hadn't started choking him and Doriana hadn't hit the button, then probably none of that would have happened.
In Survivor's Quest, the pilot Chak Fel, commanding the four Aurek Seven stormtroopers and fighting alongside General Drask, who doesn't like him but does have experience in ground fights, painfully gives command over to Drask, because his pride isn't as important as the need to fight effectively and preserve their objectives. Drask then tells him that since Fel knows the layout of Outbound Flight and Drask does not, it will be a joint command. Usually dueling egos and conflicting orders make those into disasters, but Fel knows that it won't this time, since he'll restrict himself to advising. And Drask knew he would do that. So it's not a joint command at all - it's a concession Drask is making to Fel, letting him preserve face and status, in a sign of respect.
Everything involving Dean Jinzler overcoming his old anger towards his Jedi sister and their parents.
Allegiance. The Hand of Judgment. Mara Jade saving them.
Dark Rendezvous is roughly a fifty-fifty split between Moments of Awesome from Yoda the badass Jedi Warrior, and Moments of Heartwarming from Yoda the wise and gentle teacher. The crowner has to be Yoda's little speech to Scout, a Jedi student having a crisis of confidence:
Too few Jedi I have already. But even had I a crop of thousands, small one, I would not let you go without a fight. Spirit and determination you have. Between the stars, so much darkness there is. Why would I throw away one who burns so bright?
Another one comes during an Apprentice/Padawan tournament. Since Scout is incredibly weak in the Force, though exceptional in all other areas of training, she has to resort to a clever deception against a kid who's a Force prodigy. Instead of being angry that he was beaten, especially by a duplicitous move, he smiles and says this.
Tallisabeth, being a Jedi is about being resourceful, keeping your eyes open, and never, ever giving up. You taught me a lot about being a Jedi today.
The mere fact that Scout survives the Jedi purge is kind of heartwarming—she'd been through so much hardship her whole life that it's good to know it didn't end in horror.
A very subtle one in Betrayal in the form of a callback to the Wraith Squadron books - even though they don't appear, knowing Donos and Lara end up together makes the whole ending brighter.
And Mercy Kill makes it even clearer: Lara appears (as Kirney), and not only is she obviously still with Donos all those years later, she references childrenplural.
As unpopular as the prequel trilogy is, the novelization of Revenge of the Sith is nearly a masterpiece. So much so that Matthew Stover turns the NOOOOO! scene into what it was actually intended to be. Anyway, the novel ends with this small piece:
The dark is generous, and it is patient, and it always wins—but in the heart of its strength lies weakness: one lone candle is enough to hold it back. Love is more than a candle. Love can ignite the stars.
Earlier in the book, overlapping with Tearjerker as Obi-Wan prepares to face Grievous, he contemplates the fact that he may well die. His only regret is that he'd always assumed that when he died, Anakin would be with him.
When Etain sends her marriage vows to Darman. In the same scene, when Atin also becomes married to Laseema.
The first time that Darman, Etain, and Kad are together as a family.
Knights of the Old Republic #24; Zayne shares a passionate hug with his former girlfriend; the same girlfriend who tried to murder him, who treated him with unabashed hostility, finally believes in him, meaning that Zayne has exonerated himself to one of the most important people to him; The preceding scene where she breaks down sobbing while simply saying "You didn't do it." also counts.
An issue of Star Wars Adventures goes into detail on Luke's training on Dagobah. In the film Yoda doesn't seem to recognise R2-D2 at all - turns out he did. This little gem comes while Luke is off fighting dragonsnakes:
Artoo: (worried for Luke) Bedoop?
Yoda: Worry not, my old friend. Prevail, he will. Destined for greatness. Feel it, I can.
Artoo: (rolls over to Yoda): Beep.
Yoda: Seen much have we, Artoo. Been part of much. Your part will continue. His part is just beginning. But my part, soon, will come to an end.
In a one-shot issue of Star Wars simply called Jango Fett, Jango tells his droid caretaker how he hates leaving Boba for long periods of time. He wishes that he could just sit down and be a father for a while, but his last job ended without him getting paid and he needs to make up for lost credits. Then he goes over to his five-year-old son, who is playing with action figures (and, in a CMOH all of its own, one of them is a model of Jango Fett himself), and tells him that he has to go again. The dejected Boba asks if he has to leave right then, and Jango smiles and says "No. Not right now," as the next page shows him playing with his son.
In a Star Wars: Empire comic arc detailing the backstory of Biggs Darklighter, Biggs and some friends jump ship after being discovered by a fellow Imperial Officer and brown noser Derek "Hobbie" Klivian plotting to mutiny. After trying unsuccessfully to find rebels, smugglers, or anyone that could help them (they are confined in TIE Fighters, unable to travel very far, and air is running out), they return to the ship, planning to steal more fuel and air and leave again before the crew knows what's going on. However, they find it full of signs of battle damage, far more than they had caused when they left. On the bridge, a badly injured but stable Klivian greets them and tells them that if they'd let him get out a word before trying to slit his throat, they would have learned that they weren't the only cell with Rebel sympathies on the ship. He then asks if Biggs is going to pull rank and assume command. Biggs, who had hated Hobbie since first meeting him, says that it seemed to him that Hobbie had earned command of the ship, and salutes him. This marks the beginning of a deep friendship between the two.
In Jango Fett: Open Seasons, Jango has to watch his mentor and surrogate father gunned down because Montross, a volatile and cruel Mandalorian, flies away instead of helping him. When Jango appears in front of Montross (who thought he was dead), he says that first they're going to get Jaster's body off that rock, then they're going to hunt the man who killed him. Montross, trying to appear sympathetic, tells Jango that he has a chance to do right by Jaster, and that he should be in charge. Jango tells him that that's not his call to make, and reveals to the mercenaries that Montross abandoned Jaster to die alone. At that moment, Silas, an injured Mandalorian that Jango had been supporting, pulls his blaster on Montross and says, "I'll follow Jango Fett, and no one else." It's such an "I've got your back" moment of camaraderie that it has to invoke a CMOH.
And immediately afterwards, Montross tells Jango that he's crazy and the others will never follow him. The next panel, Montross is surrounded by Mandalorians all pointing their guns at him. Same as above for why this is a CMOH.
A handful of Star Wars stories endeavored to show the men behind the masks in the Imperial ranks. In many cases, the stormtroopers and junior officers were good or at least decent men, just trying to do what they thought was right or make a life for themselves. One story in particular has a small contingent of soldiers in a small outpost under siege from hundreds of tribal natives, a la Zulu. When it comes down to the final battle, the men display a depth of camaraderie and brotherhood as they fight for their lives that is truly heartwarming, despite the grim setting.
A moment that became a bit Heartwarming in Hindsight, as well as a Tear Jerker; in one of the old Marvel Star Wars annuals, Darth Vader finds a rebel wannabe weeping over their dead mother. The comic has a bait-and-switch moment not showing that it's Vader who approaches and sympathizes, telling him that he himself was once in that position, but no, that's Vader. What makes this unintentional is that we're meant to think Vader's lying to gain his trust...but after Attack of the Clones came out, it looks more like he's reliving the horrible memories of his mother dying in his arms, and he really does feel his pain after all...
Shatterpoint is basically one long Moment of Awesome for Mace Windu. Tough, stoic, Master Swordsman, all that. At one point, he goes to save some children from being killed by a volcano, and the following conversation occurs.
Keela: I'm afraid.
Mace: Me, too. But you have to act brave. Pretend. So you don't scare the little boys. Okay?
Keela: I-I-you're scared, too?
Mace: Shhh. That's a secret. Just between us. Come on, up you go.
If it were up to him, no one would hurt anyone. Anywhere. Ever.