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 cries when Miaka leaves him despite the major brainwash he suffered from Nakago that made him hurt her. Granted, this is pretty typical of him, but all the same...
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 haven't really betrayed me. You wouldn't do that. You see? You know better than Tamahome does because I've know you longer since we're little kids together. It's just hurt so much. It's like I was getting filthier and filthier and I didn't seemed to be any room for me in your life once Tamahome comes.
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.