While they have broken up by the time the game starts, it seems a bit heartwarming that, after what happened to Nicole, Issac finally managed to move on somewhat with Ellie. It was nice seeing how far Isaac would go for her. With a gun to his head, Isaac staunchly refuses to help EarthGov. As soon as Ellie's name is brought up, however, he jumps at the call.
Not to mention that the first text log you find in the game shows that Isaac made it up to Ellie's losing an eye in the second game by buying her a cybernetic replacement, which is also a nice Call Back to how she said Isaac owed her a new eye.
The scavenger bot is a heartwarming addition to the series. It felt like no matter what happened in the game, you always had a cute little buddy to help you out.
When you are in the alien machine/city, look closely at the giant remains of the aliens: They're holding hands. There's something so human and heartwarming about such a simple gesture, especially considering the backstory behind them.
The fact that they did all they did to stop the Moon in their orbit, and warn future civilizations about the Markers and the Brethren Moons, is also rather heartwarming. They knew their race was screwed, they had no personal stake in the future of life in the galaxy, but went through an incredible self-sacrifice to stop the Moon from causing any more damage and to try and help any future civilizations from suffering the same fate.
The fact that Carver ultimately subverts the Armies are Evil trope. It doesn't seem likely at first; he beats and then conscripts Isaac at gunpoint as a first impression, and continues to act blunt and callous as they work together. Furthermore, his commanding officer is a Jerkass and the EarthGov military he is part of has a checkered past. With the setting of Dead Space being as cynical as it is, you were likely fully expecting Carver to betray Isaac in the end, maybe even having co-op players fight each other as the final challenge. Imagine the shock when Carver ultimately proved to be completely loyal and selflessly motivated, providing a solid example of Rousseau Was Right in a series where humans are typicaly assumed to be bastards.
Carver: I'm not a good man, Isaac.
Isaac: Good men mean well. We just don't always end up doing well.
Near the end of Chapter 6, after fetching a shuttle and escaping a group of regenerating Necromorphs, Isaac is blasted into space. The first thing you hear? Everyone (save Norton) is cheering for you, even Carver, who seems to shout, "Atta boy, Isaac!"