Benji's insistence in sticking with Ethan throughout the movie, despite Ethan himself trying to push him back to the CIA for his own safety. It shows both how Benji isn't even remotely a coward and that they really are good friends.
Kudos to Simon Pegg's acting here — the fact that Benji pretty much tears up as he angrily refuses to sell out Ethan to the CIA to avoid being branded a traitor, not only because he's an IMF field agent still loyal to his old team, but also because Ethan’s his friend and there’s no way he’s leaving him to face the Syndicate on his own, makes this scene a definite CMOH.
Ethan: I can't protect you, and that is why I need you to leave. Benji: That's not your decision to make, Ethan! I am a field agent, I know the risks. More than that, I am your friend, no matter what I tell the polygraph every week. Now you called me because you needed my help, and you still do. So I am staying. And that is all we are going to say about that.
This is even more heartwarming when compared alongside his earlier "truthful" statement made during Hunley's polygraph:
Benji: You seem to think I have some kind of obligation to [Hunt]. Nothing could be further from the truth... We are not friends. I owe him nothing.
Also, related to this, Ethan's insistence that Benji deliberately tells the CIA that Ethan is exactly the danger they’ve believed him to be all this time (potentially endangering his own life) so Benji is kept safe.
Ethan: Once you’re [in DC], you’ll have to inform on me. Benji: I’m sorry — what? Ethan: Just tell the truth. You came to Vienna believing you won two tickets to the opera. I attempted to recruit you into an attempt to assassinate the chancellor... Benji:[interrupting] That is, Ethan, that is not the truth... Ethan:[determined] Your life depends on them believing you Benji, it’ll go easier if you tell them what they want to hear.
After Ethan captures Lane, Ilsa gives Ethan a passionate hug before she and Ethan depart.
Ilsa diving into the underwater databank to rescue the drowning Hunt, even though she has problems holding her breath underwater. The heartwarming part is that she doesn't even have to do this. Benji already got the data, the mission was already a success. She could've just let Ethan to his fate, steal the data from Benji, and escape, but she jumps in to save him anyway with no hesitation.
The relationship between Ethan and Ilsa in general and the fact that they do not kiss at all in the movie. It just spells out that their relationship is utterly based on respect. By the time they are on the brink of their Relationship Upgrade at the end of the next film, Fallout, it feels absolutely earned.
For example: the scene at the end of the motorcycle chase, when Ilsa stops in the middle of the road and Ethan crashes his bike to not hit her. After that, Ilsa gives Ethan a long, almost apologising look before she finally drives away.
The fact that despite all that Director Hunley and the CIA have done to thwart Ethan and Brandt, not only do they arrange it to make it look like Hunley saves the Prime Minister from Atlee and The Syndicate, but also arrange for him to become the new Secretary in charge of overseeing the re-established IMF.
When Brandt recruits Luther, who retired when the CIA took over IMF, what gets the former agent to trust Brandt (considering they only met briefly at the end of Ghost Protocol and given that Brandt now works for Hunley and the CIA) is their shared concern over Ethan and Benji's safety after Brandt reveals Hunley has issued a shoot-to-kill order on both of them.
As well, Luther warning Brandt with just a look about what's in store for him if it turns out he's being used to bring Ethan and Benji in.
When Ethan approaches Benji who is strapped to a time bomb, Ilsa tells Ethan that the bomb will go off if she won't shoot him and Benji after getting the disk as she was ordered, as a final test for her. Benji then looks at Ethan teary-eyed and terrified, and Ethan puts his hand on Benji's shoulder in a small, comforting, and utterly heartwarming gesture.
