The Sea Emperor finally seeing her babies hatch and getting a brief moment to nuzzle them. Though it quickly descends into Tear Jerker territory.
The Cuddle Fish is a living moment of heartwarming. As an unhatched baby, it's absolutely precious, and it remains cute even when it grows up. You can play with it, feed it treats, pet it, etc.
You can also bid it farewell before leaving the planet. It curls its tentacles around your arm and nuzzles your hand, smiling the whole time. It's a bit of a Tear Jerker, but it also makes it very plain how much the little darling loves you.
While slightly cruel, it's definitely being Cruel to Be Kind - never releasing the Cuddlefish into open water after it hatches, allowing you to keep it in your inventory as you leave the planet. With any luck, the company will let you keep the original in return for breeding more.
Overlapping with Tear Jerker: the Sea Emperor Leviathan has one last message for you at the end.
"What is a wave without the ocean? A beginning without an end? They are different, but they go together. Now you go among the stars, and I fall among the sand. We are different. But we go... together."
The Sunbeam's efforts to rescue the Aurora survivor. While the captain's original response to the SOS is dismissive, once his ship picks up the debris field and he realizes the dire situation, his next message is laced with My God, What Have I Done? for his prior rudeness, and the Sunbeam then comes for you as quickly as possible. His next message tries to cheer you up, and in most playthroughs as his ship approaches the landing site he expresses amazement that the survivor has held out as long as they have. Alternatively, if an orbital debris field blocks their approach, he vows to inform Alterra as soon as possible and tells you to hang in there.
It's minor, but fixing the drive core shielding aboard the Aurora gets you a nice little musical sting—a very peaceful tune. It's a sweet moment that's a breather in between knifing bleeders, dodging Reapers, and putting out fires, and you really get the sense that you've helped the wildlife of the planet for the first time.
The musical cue comes back when you hatch the Sea Emperor Leviathan's babies, and they all snuggle up to her.
In one of the game's alien artifact display cases is what the database interprets as an alien translation device. In the data the words CHBCLive is found over and over. This is an affectionate easter egg the developers included for the real life CHBCLive, a Subnautica fan in China who provide Chinese translations of the game so audiences in China could keep up with it's development but sadly passed away from cancer just before the game was released to the public.
In a meta-sense, the YouTube community that helped promote the game. The developers have stated that Subnautica was at one point a last ditch effort for their studio to stay solvent as the developer was slowly sliding into bankruptcy. However, several prominent YouTubers picked up the game and started following its development from the alpha stages. This made interest in the game as well as crowdfunding absolutely explode, which pulled them back from the edge and helped make the game a runaway success.
Subnautica: Below Zero
The friendship that forms between AL-AN and Robin. In the end, she chooses to go with him back to his home planet, to learn more about the Architects (and also she doesn't have another way off the planet). The last lines of the expansion are very sweet:
Robin: And if they [the other Architects] survived?
AL-AN: With you, I am ready to face whatever awaits.
The Big Sister Worship Robin has for her sister Sam, no matter what. Even after Robin learns about what happened to the Frozen Leviathan and what Sam did to save everyone, her (and Sam's) only regret is that they didn't spend more time together.