The rebuilding of Serenity in the end. Even Inara does her part.
When the Reavers attack the first time, River collapses in a fit. Jayne instantly runs over to her side and asks if she's alright as well as holding her.
The first 40 minutes pretty much confirm that Mal for one still doesn't trust River 100%. At the end of the movie... he's letting her drive.
Shortly after Simon decides that he and River are leaving Serenity, River's programming is triggered. She goes absolutely nuts and beats the living snot out of everyone in Fanty and Mingo's bar. Simon says a "safe word" that causes her to collapse. What does Mal do? Calmly, without saying a word, picks River up and carries her back to Serenity.
It says a lot that the movie itself could be considered a meta-example. After responding to the fan petition, Joss Whedon started seeking out a way to make this movie, and Alan Tudyk decided to return a prop he reportedly filched off the Firefly set - the Big Red Button used in "Out of Gas", with a note quoting that ep: "when your miracle gets here, hit this button."
It's easy to miss, but while Serenity is plummeting toward Mr. Universe's planet, Jayne is checking the passengers' seat belts before he gets a chance to strap himself in.
Including River's! I'm not sure about Simon's, but I do recall seeing him passing by River's belt to make sure it was done in. And if I recall, either River or Inara (I forget who) calls out for Jayne when he starts getting thrown around in the room when the ship is spinning out of control. Neither one of them had any reason to like him whatsoever, but yet they still care about each other when it counts.
The final scene with Mal and River flying, when River asks him to say the words she knows anyway:
Mal: Love. You can learn all the math in the 'verse... but you take a boat in the air that you don't love... she'll shake you off just as sure as the turn of the worlds. Love keeps her in the air when she ought to fall down... tells you she's hurting before she keels. Makes her a home.
Mal calling River a "little albatross".
Let's not forget how River's Crowning Moment of Awesome - taking on an entire room full of Reavers and winning - was born of a desire to protect her brother and friends the way they've protected her.
Special points to the ship flying away. The image of a multi-ton replica of a crippled bird in cast iron, a thing that doesn't look like it should ever be able to fly, that crashed, not only achieving flight, but apparently punching physics in the face while doing so. It has done the impossible, and that makes it beautiful.
When Mal is talking to Inara right before she hints that she'll be staying on Serentity, Mal gently touches the cut on her lip. Yes, they both play it off, but its just like the moment in Out Of Gas when Mal touches her shoulder: a small gesture that says everything he can't.