In one room, Dio can invite K with a drink, apparently genuinely forgetting that his unremovable headgear prevents him from consuming solid or liquid aliments.
Quark's letter to Sigma in Tenmyouji's ending, which details his relationship with Tenmyouji.
K's story as revealed in his path, which is mixed with Tear Jerker: After finally getting a surrogate mother in Rhizome-9 in the form of Akane, the 18 year old Kyle finally experiences true happiness in his family.
In what doubles as a Tear Jerker, the password of the old woman is Jumpydoll. "Jumpy" was Akane's nickname for Junpei when they were children, and her most treasured possession was the doll he gave her as a parting gift. Akane never forgot about Junpei, even after all those years.
A Heartwarming in Hindsight moment comes after playing through Zero Time Dilemma. The ring Akane wears? It was given to her by Junpei during the Decision Game, and she's worn it ever since, on the wrong hand, even after erasing Junpei's memories. This, coupled with the hologram's message for Tenmyouji, and it's easy to see why he cries.
Quark's ending. Knowing full-well that Dio will choose "betray", Sigma chooses "ally" to get Dio to give up the Axelavir to save Quark's life, even though this means his BP will drop to -1. This also leads to an Awesome Moment where Sigma forces Dio to hand over the Axelavir even after being injected with the Soporil, then keeps Dio from going through the Number 9 door just long enough for it to crush his arm. When he wakes up, there's a stump where his arm should be, but the others are relieved to see him, including Quark, who thanks Sigma for doing what he did. It's very sweet. Then things promptly go to hell when Alice displays Radical-6 symptoms.
In Alice's ending, she has just betrayed you again. She plays it cool, but once she and Sigma are alone, she breaks down and confesses that she feels horrible about it and admits that Sigma would be justified if he killed her right there. Sigma does not and instead forgives her.
Luna's ending: "Would you...hug me?"
In the true ending, Everyone (except Dio, who is kept unconscious) agrees to play the Ambidex Game over and over with everyone picking Ally until all of them have enough BP to escape. And they actually do it, with nobody giving in to the urge to open the number 9 door before everyone else can. This is the only ending in which this happens—in every other ending where somebody gets 9 BP, he or she immediately opens the door and escapes, abandoning the others (or in the case of Sigma, being held down by the others while Clover escapes or getting knocked out and possibly having his arm removed to steal his bracelet).
In order to get Dio's "good" ending, you have to choose "betray" against Clover, who is already distraught over Alice's death. If you choose "ally" instead, you get Dio's bad ending, but Clover is clearly touched and thanks Sigma for it.
In Sigma's ending, when Luna and Sigma talk in the garden and she wonders whether or not he may be a robot. Sigma asks if she isn't afraid of him, since - if that were the case - it's possible he's being controlled by Zero. Her response is that she even if he were, she wouldn't be scared. Why? "Maybe because you're a robot." Now, how does that dialogue in Luna's ending go again?