Niccolo's Pet the Dog moment with Marco on their initial journey east, stopping in place indefinitely to give his son time to recover from his ailment, and telling his brother to Get Out! for suggesting they leave him behind.
Ariq and Kublai's final conversation the night before their fight. They may be about to fight to the death, but instead of talking like they despise each other, they just talk like brothers. They discuss their mother. Ariq talks about when Kublai went missing and he planned to go find him. They discuss Ariq's desire for Mongolia and Kublai tells him he can never have it for himself. The two of them bow heads and embrace and that is that. They part as brothers. It's a very touching scene.
Byamba expressing his genuine appreciation toward Marco Polo for risking his life to save his father, Kublai Khan. Since his arrival in Mongol up until before this, Marco had been receiving nothing but hostilities and negative treatments from pretty much everyone else. This include Prince Jingim, who was even more hostile toward Marco even though the guy just save his father. Marco, in return, stick with Byamba and refuse to leave him behind when they encouter the Old Man
Byamba: Has anyone ever thank you...for saving my Father's life?
Bymaba: The point of all this is to thank you. So...Thank you.
When Marco is facing a death sentence over the failed attack on the walled city you can tell Hundred Eyes is genuinely distraught upon hearing the news. He even goes as far as to personally implicate himself to the Khan with being complicit in Polo's accused failure.
Jingim finally reconciling with Marco, and seeing him as someone to trust rather than resent.
Season 2:
Marco's reunion with Hundred Eyes after the campaign south. It's brief, but Hundred Eyes smiles (which he pretty much never does) when he hears Marco at the door. And Marco even brought him wine from his home region, which he deeply enjoys. Thus, the two of them begin Season 2 in comfortable friendship.
Kublai's knighting of Marco, after bringing him on his soul-searching journey into the woods. It really goes to show how far Marco's gone in earning the Khan's trust.
Hundred Eyes, when doubting his own loyalty, and possibly preparing to say goodbye to his students under the Khan, thanking Prince Jingim for saving his life long before, and telling him that he'll make a fine emperor one day.
Mei Lin's reunion with her daughter. And afterward, when she kisses Marco in thanks. Unlike all the previous times she's kissed someone, she's not putting on a show of attractiveness. It's brief, and rather friendly, and very genuine.
The birth of Kokachin and Jingim's child. There are heartwarming moments all around, but especially with Jingim's parents — Kublai overcomes his post-battle Heroic BSoD to come spend time with his son, and Chabi helps midwife for Kokachin. In Kublai's case, it's undercut a little by his words of comfort degenerating into a rant about foreigners, but he's obviously expressing his grief at Ahmad's betrayal more than anything else. And it's interrupted by Chabi coming in and asking for, of all people, Marco's help. At the end of the day, they are a family, and it shows.
Kublai and Chabi reconciling after the truth comes out about Chabi's scheme to force an heir. Chabi is overcome with grief, believing she's destroyed her family — but Kublai realizes, slowly and steadily, that Chabi has done the exact thing that he would have wished, without his asking or even knowing. After an entire season of discord between them, they finally see eye to eye.
