Heartwarming / Inheritance Cycle

Eragon

• Brom dies when he jumps in front of a dagger thrown by the Ra'zac to save Eragon.
• Murtagh deciding to come rescue Eragon from Gilead, and then join up with him in running to the Varden. Yes, he admits he didn't want to do it and he's angry with Eragon for forcing him, but he still does it.
• Eragon rescues Arya and that evening while securing her, he notices she's been tortured. While healing her, he's so disgusted at their number and brutality that he vows he'll kill the person that did this to her. And since he kills Durza later, he does!

Eldest

• Eragon gets formally adopted into the clan of King Hrothgar. While it is a gesture primarily meant to ally the new Dragon Rider to the dwarves alongside all the other races, it does seem to have some sincere affection, and Orik joyfully notes that this makes them brothers!
• When they arrive at the elves', we find out Arya is the daughter of the queen, and that they were estranged up until this moment! Her mother tearfully hugs her and declares this a happy day.
• The big reveal - there's another dragon rider with the elves! Eragon isn't alone! He has a teacher! He's so relieved it isn't all on his back that he falls to his knees, weeping.
• The Agaeti Blodhren. Eragon has been having terrible seizures more than once a day from his back scar, even more from a regular injury, a final curse from Durza. It's reaching the point where he's basically disabled, and wondering how he's ever going to be effective on the battlefield if he could keel over at any moment. The doubt is tearing him apart. And then during the Agaeti Blodhren, the most sacred festival of the elves, two twin elf women with an intertwining dragon tattoo spanning their bodies perform a special dance that culminates with the dragon jumping off their skin, turning to Eragon, and breathing a blessing onto him. The end result? He's rejuvenated, given some elfin qualities like their strength and speed, and most importantly, his back scar is removed. He'll no longer have the seizures! He weeps a little at this, too.

  "Our gift to you. To do what you must."

• Eragon finally works up the courage to come onto Arya during the festival. It doesn't work. She even rejects him kind of harshly. But she eventually makes it clear that they're still going to work together, and she does have some respect and affection for him. Just definitely not in that way.
• Eragon and his brother Roran are finally reunited after over a year. A happy moment for both.

Brisingr

• Eragon and Roran finally kill the Ra'zac after they killed their father/uncle and spearheaded the destruction of their home. "For my father! For Carvahall!"
• Eragon stays behind when Roran and Katrina and Saphira leave so he can solve a complicated moral dilemma. When they return and tell the Varden, Arya immediately leaves and tracks far into the empire's territory to find him. Yes, he could probably make it back himself, and yes he is a strategic asset, but they could've sent someone else who wasn't also a chief liaison and daughter of the elf queen. Despite rebuffing him romantically earlier, when push comes to shove, she does feel responsible for him a bit.
• Later, when they unite and are tracking through enemy territory, they end up spending a long night in front of a fire just chatting about life like friends do. While their relationship was a little cool after he came onto her, and she was a little skittish around him, the conversation shows they genuinely can be friends despite their age gap and history. They even end up confiding in each other quite a bit. It's a friendship that never could have happened before.
• Roran and Katrina finally get married, with Horst standing in for Roran's father and Eragon officiating.
• Eragon and Saphira are separated for an extended period of time while he's away overseeing the dwarf coronation. The two race to each other when she's close and have a sincere and loving embrace.
• In the climax, the enemy have summoned a Shade to turn the tide, but Arya and Eragon are such a good tag team that Arya manages to kill it. Eragon even tells her afterward that this was just a repeat of last time - he never would've killed Durza if she hadn't distracted him back when.

  Eragon: Now I shall have to call you Shadeslayer.

Inheritance

• When Nasuada gets captured by the Empire, she withstands an ungodly amount of torture by Galbatorix himself. Her only solace is an unexpected ally: Murtagh. He heals her after her torture sessions, talks to her, weeps for her pain, and explains that he was the one responsible for not only her capture, but also her survival. Galbatorix was going to send the Black Hand to kill Nasuada, but Murtagh convinced him to capture her instead. He contacts her with his mind and warns her whenever Galbatorix is about to make her hallucinate. He holds her as she cries after a particular Nightmare Fuel-tastic torture session involving burrowing worms and promises her he'll figure a way to get her out of there. During Murtagh and Eragon's duel, the only reason Murtagh is so furious is because if he'd just waited another day, Murtagh was going to get Nasuada out. And the only way they ultimately defeat Galbatorix in the end is because Murtagh turned on him because his true name had changed- for her. Definitely a CMOH for Murty, and officially confirms the Murtagh/Nasuada ship.
• Eragon entering Urgals and dwarves into the bond with dragons, so that all four main races of Alagaesia can become Dragon Riders.
• Eragon and Arya KIND OF get their ship confirmed. The last dragon hatches for her. Their dragons are attracted to each other and seem to even be mating. And Galbatorix is dead. The war is won. Eragon has done everything she hoped he might. Things really are different. And she admits she feels something. And while they still agree the age gap is too large, she hints that maybe in the future, in a few more years, when he's had a couple decades to get older, something might happen. That's probably about the best Eragon's going to get at this point.
• That after everything that happened to Roran he can still go home to his wife and daughter and still live the life of a farmer.

The Movie

• When, after Eragon wakes up, not certain of Saphira's fate, sees her come in for a landing, right next to his bedside. She even scolds him for his recklessness. Yep, everything's back to normal.