At the start, when they think the Chief's dead or incapacitated, Johnson wants heavy lift equipment, because "We're not leaving him here." And then the Chief's hand grabs him, and he speaks up, and Johnson gets cheerful. Less glomy. Whatever. Point is, it's a great demonstration of comradery.
Cortana the level, when you reach Cortana the person.
Cortana: "You...keep it. I do know how to pick 'em."
John-117: "Lucky me."
As if that wasn't wonderful enough, keeping in mind the background from the Fall of Reach novel makes it even better.
The departure of the Sangheili at the end.
Rtas 'Vadum: Things look different, without the Prophets' lies clouding my vision. I would like to see our own world. To know that it is safe.
Arbiter: Fear not. For we have made it so.
At the credits of Halo: Reach, Bungie gives a goodbye letter to its fans. No true Halo fan could read it without breaking into tears.
At the end of Halo: Reach, we see Reach...in 2589. The grass is green. Snow sits on the mountains. And Noble Six's helmet still lies where it fell, and Dr. Halsey's voice speaks over the peaceful vista, telling you that your death was not in vain, and that through your courage, humanity was ultimately able to survive and rebuild.
Pretty much every scene Master Chief interacts with Cortana is this. Especially when she finally manages to touch him, right before she dies.
When John learns that Cortana is suffering from rampanacy, the Master Chief's immediate reaction is that if he can get her to Catherine Halsey, she'll be able to repair Cortana. It's heartwarming because despite the backdraft Halsey has been receiving from Halo canon over the last few years, the scene is a stark reminder that John will never lose faith in her.
More than just lose faith in her, it smacks of "we'll take you to mommy, mommy will make you all better".long awaited acknowledgement in the games what was established in the books: the Spartans think of Halsey as their mother.
The Forerunner Saga
Humans and Forerunners finally come together on friendly terms following the Halos firing. They both attend a ceremony and mourn and even dance together. Trial, a Lifeworker overseeing humanity, has this exchange with Riser:
Trial: "You know, humans and Forerunners were always meant to be brothers, not to fight like we did."
Riser: "Brothers fight too, you know."
Then, when humans are brought to earth, Riser and Bornstellar share some parting words:
Bornstellar: *In regards to the Portal on earth* "Perhaps one day your children will make their way back, and I hope meet our children"
Riser: "I doubt even I will live long enough to see that day. But it is good to think that one day our young will rise to another challenge as brothers should: making trouble, finding strength."