The True Ending of, or hell, the entire second half of the Kohaku route. After everything Kohaku goes through in life, and the mental trauma she endured, Shiki shows her the love she desired her entire life, being given a reason to truly be happy. The True End to her route has brought nearly everyone that's seen it to tears of happiness.
Both dampened and heightened to some degree by the fact that to see that ending, you have to go through Hisui's route first, the ending of which is ice-cold and deadly.
Correction: the Hisui True ending is ice-cold and deadly, yet her Good Ending is one of the most heartwarming moment in the entire game.
While leading to a Tearjerker, Akiha shielding Kohaku from SHIKI's attack shows that Shiki wasn't the only person Akiha cared about. It becomes even more Heartwarming In Hindsight when its revealed that Akiha knew about Kohaku's plan for revenge against the Tohno family meaning that she knowingly took the bullet for someone who wanted her and her blood brother dead.
Also, the Drinking, Dreaming Moon secret side-story in Kagetsu Tohya.
Also in regards to SHIKI, in the side-story "The Tohno Family Con Game," all the characters are participating in a game of tag, SHIKI hears Akiha screaming and doesn't hesitate to rush to her aid while Shiki prepares to escape out a window warning him that its very likely a trap. SHIKI responds by saying even if it is a trap he'll protect Akiha no matter what. Sure enough, he gets tagged. It's a sweet moment since its probably one of the few times SHIKI doesn't speak of Akiha in a possessive manner and does show a genuine Big Brother Instinct towards her. Makes one wonder how things could have turned out if he hadn't inverted or been possessed by a vampire.
The manga adaptation (which follows Arcueid's route) turns the Bittersweet Ending of her True End into a happy one. Shiki, some time after talking with Aoko for the last time (as in the Eclipse epilogue) and donning his Satsujinki outfit, finally reaches the Millennium Castle with help from Ciel, wakes Arcueid up after slashing away the chains binding her, and promises to live with her thereafter. The two subsequently greet the rising sun on the castle balcony holding each other.
One big moment is when the UST between Shiki and Arcueid is resolved.
Then there's the game's other big one. It might be when Shiki returns Kohaku's ribbon, proving that he recognized her and remembered his promise to her, prompting the still emotionless Kohaku to start crying. Or it might be that, despite everything that's happened in her past and despite everything that's happened in other routes, Kohaku gets a happy ending. Not a bittersweet ending. A happy ending!