Astolfo saving Homunculus from death at the hands of his would-be Homunculi captors, then bringing him to Chiron's room, where Chiron heals him. When Chiron asks him why, he simply answers "Because I could" with a big smile.
Astolfo's speech to Saber of Black, followed by Siegfried's sacrifice.
"We took form in this world to have our wishes granted... but that doesn't mean we can just accept anything that happens! Have you forgotten how to be a hero?! I haven't! I am Servant Rider... but I was Charlemagne's paladin, Astolfo! And I won't abandon him! I won't!"
Sieg carrying a starving Jeanne on his back until they find a place to eat, and then having a moment of Sleep Cute on the same bed... Which they both fall off of.
Shirou Kotomine innocently dreaming of his past, sleeping on Semiramis's lap.
Pretty much any interaction between Shisigou and Mordred, as they quickly pick up a very endearing father/daughter dynamic.
During the massive free-for-all between the Black and Red Factions, Sieg shows up to the battlefield and spends some time bandaging a few of the surviving homunculi. Considering the fact almost everyone, including the homunculi themselves, see them as expendable troops makes this moment a very humanizing moment for Sieg, who's only trying to impart some of the mercy he received from Astolfo and Siegfried to his fellows.
When he sees Astolfo in trouble with the Red Faction, Sieg wants to help him, but hesitates because his original goal was to save his fellow Homunculi. They encourage him go save Astolfo because he's free to do so.
A minor one, but Semiramis willing to support Mordred during her battle with Sieg, despite her being the only Servant from the Red Faction not to be placed under Shirou Kotomine‘s control.
Even though Mordred and Sieg aren't friends, you can't helped be amazed at how Mordred readily defended Sieg by decapitating the sadistic Celenike for trying to force her Servant to harm a homunculus who was basically a child. As a victim of child abuse, Mordred knew that experience all too well and won't let it be thrust upon anyone, not even her enemies.
When it seems that Astolfo will disappear with the death of Celenike, Sieg decides to form a contract with the one who rescued him from imprisonment.
The relationships that grow between Masters and Servants.
Mordred had a rough life with a manipulative mother and her father who practically shunned her. Thankfully, when Kairi summons Mordred, he treats like a daughter. Mordred would stop fighting and made sure her Master was safe.
Frankenstein's Monster was abandoned by her creator. Her Master, Caules does what her creator never would: treating her as a person. Also, the scene where she offers him a flower.
Despite its disturbing nature, Jack the Ripper has a mother after a long and bloodstained search.
The interactions between Caules and Chiron look like those of guy getting along with his sister's boyfriend.
Jeanne is clearly touched when Sieg says he's worried about both her and Leticia, the girl she's possessing.
In a weird way, Reika's final moments with Jack. When she sees Atalanta targeting Jack behind her, she doesn't panic or try to worry Jack. She stays calm, assures an unaware Jack that she'll of course play piano for her more later, then quickly drops Jack behind her and puts herself in the path of Atalanta's arrow. Even as she's dying, she continues to comfort Jack and uses her remaining Command Seals to ensure Jack lives for as long as possible after her. Crazy person or not, she was a good mother to her surrogate daughter.
Surprisingly Jack's ghosts accepting that they can not be saved and willingly letting Jeanne exorcise them.
Jeanne: One day I hope your souls find rest. I shall pray for each of you.
Jeanne's reply to Jack asking if it makes her sad. Not at all. Everyone of you is headed somewhere you belong. So there is nothing to be sad about.
Karna lives up his epithet "Hero of Charity". Despite not being linked with his original Master, he asked Caules to save the original Masters anyway, before he goes on to commence an all out battle against Sieg for the sake of his warrior pride, regardless of his 'fake' status. Though he was actually defeated not with Sieg's power alone, but Astolfo carrying Achilles' Noble Phantasm (so technically it's 3 vs 1), he still commended his opponents as he perished standing up with a smile while bleeding his mouth. Even Astolfo had to commend him... and he still denied credit.
Sieg is slightly ashamed because he and Karna had promised to fight one on one, but he needed Astolfo's help to beat him. Karna tells him there is no shame, because they had also promised to fight at full power, and as his servant, Astolfo was rightfully part of Sieg's power.
After discarding his Noble Phantasm to Astolfo which was then used to help defeat Karna, Achilles, knowing that his immortality has been removed due to his fight against Chiron, goes to interrupt the battle between Jeanne and Atalanta. He does this for one reason: He wanted to set Atalanta straight after her fall to madness. It's clear that he really cared about her. They ended up doing a Mutual Kill, but Achilles was satisfied with the results: Atalanta recovered to her usual calm self before dying.
In the middle of the battle against Semiramis, Mordred realized her true goal... and somehow it wasn't that selfish, considering her reputation as the Knight of Treachery: She realized that taking up Caliburn would mean being isolated and discarding one's humanity, yet Arturia took the burden for the sake of the people. So Mordred wanted to become a King... just to spare Arturia from that fate. In the end, Knight of Treachery or not, Mordred really loves her father...
Mordred refusing to abandon Kairi and instead choosing to die with him.
In episode 24, Caules realizes Sieg being revived by Blasted Tree earlier in the story triggered the Noble Phantasm's rare second effect and gave him Fran's abilities. Or as he sees it, Fran is helping Sieg face Shirou.
"GO GET HIM, BERSERKER!"
We have Gilles, after it was known that the version summoned by Shakespeare was in fact the Serial Killer version before he regressed further into the Caster version, being given a second chance to redeem his heavy sins in the eyes of God by Jeanne by defending her as she prepared for her second Noble Phantasm. He took the chance with gusto.
Gilles: For me, this is enough...
The I Will Wait for You moment in the finale. Sieg has spent years in the Reverse Side of the World, in dragon form, keeping the Greater Grail there so it can't fulfill Shirou's wish. Jeanne is able to break through into the Reverse Side via the Throne of Heroes and reunite with him. There she reverts him back to his true form and confesses her love to him. It's similar to, and is likely a throwback to, Shirou and Saber reuniting during the true ending of the Fate route in Fate/stay night.
Semiramis and Shirou having a Together in Death moment in the end and it is full of heartwarming.
Together with funny, Semiramis asks Shirou what he was planning to do with her after he his plan had succeeded. A saved world has no need for an empress, so he never had any intention giving her such a position. Would he betray her? No. He would apologize. He's kinda sheepish about it and she forgives him with good humor. It is very much like a married couple with a minor spat.
Semiramis kisses Shirou as both of them fade and the Hanging Gardens collapse, admitting her loyalty and love to Shirou. He thanks her for it, which is something no one else has done, given that she is known as a poisonous assassin.
Shirou passed away in peace, content with what has transpired even in his defeat and thanking Semiramis for her services. This is pretty prevalent for Semiramis, who's usually referred as a treacherous person, she finally found someone she wouldn't betray.
In the anime, Waver has a piece of red cloth kept safe at his desk. Even if Fate/Zero never happened, he still summoned Iskandar.
Also according to the Materials books, Shirou Emiya, Rin Tohsaka and Sakura Matou live much better lives. Shirou doesn't experience the Fuyuki Fire and grows up with his birth parents, the Tohsakas have given up on the Grail and are seeking the Root via basically enlightenment using Chinese Kenpou mixed with magecraft, and since Zouken died in this timeline, Tokiomi reached out to the Edelfelts and thus Sakura Edelfelt is Luvia's adopted younger sister and wrestling tag-team partner - she even emulated Luvia's Noblewoman's Laugh. Oh, and the three are in a rom-com love triangle.
