For this troper, Ren's good end CG may be the most heartwarming thing N+C has done.
Koujaku's very awkward confession to Aoba is really cute. Being The Charmer, Koujaku has an easy time attracting women, but once he realizes that he's in love with his best friend, words fail him. The CG with Koujaku and Aoba awkwardly holding hands and blushing while the former is confessing is funny and adorable.
In RE:Connect, we learn that Koujaku has a habit of holding onto Aoba's hand before he orgasms.
Noiz's entire route. Watching them slowly warm up to each other, going from tolerating each other to genuinely falling in love, all while Aoba picks his way through Noiz's world view, and emotional defence he'd had since he was a child is very touching, and Noiz regaining his ability to feel and the honest joy he has in tiny every day things like the warmth of another person's skin is lovely. Noiz's route is very character/emotion driven and it really shows.
Also, in RE:connect: Noiz asking Tae's permission to take Aoba to Germany is very much like someone getting permission for marriage, and Aoba's hesitant, but truly honest admission to Tae that he loves Noiz and wants to be with him is incredibly sweet; especially given how unsure Aoba was about moving at the end of the last game.
So much of Clear's route. Especially Aoba convincing him to take off his mask, promising that no matter what he wouldn't hate him, then assuring him over and over that he's perfectly normal. Clear is nearly in tears by the end of the scene. Really this whole damn route could be considered one.
Also Clear's straightforward love confession, followed by a kiss. Aoba isn't yet sure how to respond, so he hugs Clear instead.
Also, back in the present time (near the end of the scenario), Tae mentioned about how she just received a postcard with no sender. But, when Aoba saw the postcard had a picture of the blue butterfly on it, he knows that it's from his parents (which reminded him of the promise his father made to him). This gave Aoba (and Tae) hope that they'll keep on waiting for their return.
In RE:connect, it's shown that Mizuki had somehow healed from the unfortunate mind rapes put upon him (though one of them was by accident). The CG in his route put a smile on this troper's face.