Any scene with Athrun and Kira re-uniting outside of the battlefield.
The scene where the Justice saves the Freedom from fire, proof that Athrun would rather defy orders than side against his friend.
Also when the Archangel and the Orb ship Kusanagi launch into space, and the Freedom reaches out towards the Justice so Athrun isn't left behind. Quite possible the greatest bro moment between two Humongous Mechas.
Captain Ramius apologizing to Kira for placing so much on his shoulders, while also thanking him for everything he did to protect the crew of the Archangel up until that point in Episode 12.
Cagalli and Kira have a few dramatic hug scenes. The strongest of which is probably when The Archangel docks in Orb for the second time, and Cagalli rushes aboard to find Kira and immediately jumps into his arms. Of course this is as far as they ever go since they're brother and sister but even so their moments are rather moving.
The Cagalli-Kira-hug heartwarming is combined with Kira-Athrun-reunion heartwarming in a particular scene after Kira and Athrun disembark from their new mechs and walk up to each other after the battle of Alaska. The situation is very awkward between the two of them, as this is the first time they meet face-to-face since they murdered each other's friends and nearly killed each other... but then Cagalli runs up from behind, hugs them both, and breaks down crying, overwhelmed with happiness at seeing both men she deeply cares for safe and, apparently, friendly.
Any of the dramatic kiss scenes. Mu and Murrue's scene (in which Mu admits he disobeyed orders and saved the Archangel from destruction simply because he loved Murrue) and Athrun and Cagalli's scene (where they vow to protect one another and finally end their Slap-Slap-Kiss with, obviously, a kiss).
In Gundam SEED, after Kira defeats Andrew Waltfeld and his lover/co-pilot Aisha, the two of them quickly jump out of their seats and into each others arms; perhaps as much heart-rending as heartwarming as the mobile suit explodes immediately afterwards, presumably killing both of them. That they wanted nothing more than to hold each other at the end so it certainly qualifies.note Andrew survives, and says that Aisha protected him at the cost of her own life, which makes it count even more.
Lacus comforting Kira after he finds out the truth about his origin, telling him that he still has a right to exist as everyone else does. It was something that she learned from her own mother who she barely knew since her childhood. Regardless of what you think or feel about Lacus, this was one of her highest points in the series.
The 1 on 1 scene where Athrun is being promoted within ZAFT after destroying the Strike and Yzak is acting unpleasant. Instead of making it harder for him, Athrun apologizes for their lost comrades and thanks him for his service. Yzak seems to take it well and tells Athrun not get himself killed, so they can keep their rivalry.
After Kira's first major battle in the Strike, Mu is called over to the Strike as Kira is refusing to come out of it. As Mu approaches and then overrides the hatch controls, he angrily calls out Kira's name, as if he's a Sergeant Rock about to chew out the New Meat. But when he sees inside and realizes Kira is nearly catatonic due to combat stress, Mu immediately switches to a much gentler voice and Big Brother Mentor demeanor, speaking encouragingly to Kira and helping him out of the cockpit.
During his period of captivity aboard the Archangel, Dearka accidentally triggers Mirallia's Berserk Button by abrasively wondering if she's an emotional wreck because "her Natural boyfriend went and got himself killed." Following Mirallia's ensuing Freak Out! (in which she tries to murder him with a knife), he realizes that she did, in fact, lose someone, and kicks himself for unwittingly taunting her about it.
The next time he sees her, he asks what her boyfriend was piloting at the time of his death. When he learns it was a Skygrasper, he concludes, with relief, that "it wasn't me." He then offers Mirallia the chance to kill him, if that's what she came to his cell to do.
During the Battle of JOSH-A, the Archangel discovers that the top brass has already evacuated their base, and that they left the remaining straggling Earth Alliance forces behind as bait to lure ZAFT forces close enough for a hidden self-destruct system to slaughter everyone, ally and foe alike. Upon hearing this, Kira (now piloting the Freedom) opens a channel to both sides, urging everyone to evacuate; Yzak isn't having any of it, and continues to bear down on him. After a brief struggle, Kira is poised for a killing blow on Yzak's cockpit and taking revenge for a civilian shuttle he had been protecting earlier in the series (Yzak had shot it down, thinking it was full of escaping Alliance soldiers). Instead, in a split-second decision, Kira angles his beam saber downward, slicing the Duel's legs off and kicking it away to be picked up by a retreating ZAFT suit. He very well could have simply taken Yzak's life there and no one would know it was for simple vengeance, but with his renewed outlook and desire to simply end the fighting, he chose not to. Someone has to end the cycle, after all.
The Manga adaptation's version of Flay's ghost appearing to Kira. Unlike the show, the manga shows Flay's ghost actually appearing to Kira and him acknowledging it. Ultimately Flay apologizes for her actions, embraces Kira and encourages him to keep fighting and not give up. Compared to the show (where Flay never gets to make amends) the manga manages to give her some small measure of redemption for her actions.
Flay Allster hearing Kira's voice and being happy that he's ALIVE. It shows how far she's come from wanting him dead.