During the infiltration of Mount Reikaku, Tamahome suddenly appears to help Miaka out despite having been imprisoned in Kutou. Sadly though, he was imprisoned in Kutou the whole time: the Tamahome who appeared was just an illusion brought about by Tasuki's talisman because Miaka had written Tamahome's name on it.
Near the end of the Kodoku arc, evil Tamahome is surprised to find himself in tears when his No-Holds-Barred Beatdown with Tasuki is over, and Miaka has left with Tasuki and Chichiri. At any other point in the series, this might have been brushed off as an ordinary event, but not after he has been left by his love for hurting not just her, but their friends as well.
The scene where Hotohori meets his son Boushin is somewhere between a CMOH and a tear-jerker. Father and son meet for the first time, and so Boushin runs into Hotohori's arms, forgetting that he is dead, and stumbles right through him instead. The prince (and every other person with a soul) begins to cry, so Taka offers to let Hotohori possess him for a while so that he can hold Boushin. When Boushin calls Hotohori "papa", which happens to be his first word... oh dear. *sobs in a corner*
Miaka rejecting Hotohori's proposal and breaking down while she's at it, feeling extremely sorry that she can't return his genuine feelings. Made even better when Hotohori reminds Miaka of her promise to help him save the empire and he says this:
Hotohori: Then please... will you allow a pathetic man like me to be in love with you once again?
Miaka and Nuriko learning that Tamahome had been his family's breadwinner all along.
Yui: I knew that you hadn't really betrayed me. I know you better than Tamahome does. Because the two of us have been together since we were children. It was just... It hurt so much. It was like only I was getting filthier and filthier. I couldn't find a place to exist between you and Tamahome.
A scene very late in the manga, when Tamahome is revealed to actually have been alive and apparently not reincarnated as Taka Sukunami. He's just as gentle with Miaka as he originally was and has all the memories of what happened (which causes a huge inferiority complex for Taka). But while Miaka realizes that he's Tamahome... she realizes she can't. She doesn't love Tamahome, she loves Taka. She loves him more than she can imagine and even seeing her beloved Tamahome in front of her makes her wish to be with him immediately and Suzaku-Seikun uses his power to teleport her out of the Shi Jin Ten Shi Sho universe into the real world and into Taka's arms.
When Tenkoh pits his Brainwashed and Crazy servant Yousui (with Tamahome's powers and memories) against Taka, in a fit of jealousy, he unleashes a mortal life force blast. Having just vowed to protect her loved ones, Miaka throws herself in the way of his attack without a thought, suffering nearly fatal wounds in the process. This is nearly enough to drive both Taka and Tamahome past the Despair Event Horizon, which would destroy them and generate such negative energy it would free Tenkoh from Suzaku's seal. But Miaka's disembodied soul cheers on Taka, once more confessing her love to him and giving him the Heroic Second Wind he needed to go on, not give into the hate, and finally overcome himself and take in Tamahome, thus becoming a complete human being.
Miaka and Taka chanting the spell to summon Suzaku together.
The ending, full stop. Seeing Taka and Miaka reunited, with knowledge of each other's marriage in the other world, is super-heartwarming, as is Tetsuya and Yui's relationship, which manages to survive as well.
The Suzaku and Seiryu warriors' trip to the hot spring omake. It's nice seeing everyone alive and stuff.