The sniper level, ending with Joel taking out the Humvee that's been plaguing them since downtown Pittsburgh by shooting the guy throwing Molotovs as he goes to throw one.
The Jackson settlement. Every other settlement and even the military relies on scavenging for supplies, and they can't exactly scavenge forever (the quarantine zones are even slowly collapsing). However, the Jackson settlement had learned how to be self-sufficient, having its own livestock and even horses to use as transport. When Joel and Ellie get there, they're in the process of getting electricity running in the power plant - and they succeed. You are even treated to a nice overhead view of the settlement later on, with lights running proudly.
Tommy: We ain't back in Boston. You lay your hands on me again and it won't end well for you.
As unexpected as it is playing as Ellie, it's awesome when you realize this little girl had to immediately take the responsibility to fend for herself, get food and medicine and protect the one you spent most of the game playing as.
Also on the subject, in the UEC science building when Joel impales himself and Ellie suddenly becomes just as lethal as him while helping him escape.
And Joel himself in the same scene, who continued to shoot and kill enemies while still impaled.
The latter part of Winter, fighting through the cannibal settlement.
Ellie: Ellie is the name of the little girl who broke your fucking finger!
On the one hand, you get Ellie fighting and killing David in what is essentially the game's only boss fight.
On the other, there's Joel moving through a snowstorm while fighting scavengers. At one point, he's proceeding on reputation alone - these people actually are afraid of the "crazy old man" and back away from him, even though he's barely recovered from getting impaled and can hardly walk.
Even though it horribly outlines how easy it is for him to kill and injure, Joel interrogating two of David's mooks. Morally Ambiguous Is Not Nice.
He later tops himself - he interrogates a Firefly by shooting him in the groin in the most matter-of-factly way possible. Of course, this alerts the others to his presence, but that's a minor detail.
The final push through the Firefly lab. You go through a hospital building filled with men armed with assault rifles, bust in just before the operation, kill the surgeon stupid enough to threaten you with a scalpel in cold blood, gently unhook Ellie from the stuff she's hooked up to and run like hell to an elevator, cradling her in your arms.
Try to do it like you're in a revenge movie, makes it even more awesome as you slam that hatchet into the last soldier who gets in your way or ambush two soldiers around a corner with a flamerthrower.
You can also do it stealthily, picking off each of the soldiers one by one without them ever seeing you. It's the climax of 28 Days Later all over again!
Saving up enough points to learn the ability that counter-attacks the Clickers One-Hit Kill move. Joel will never seem more awesome then when he pushes a Clicker back and stabs it in the throat after a whole game of being insta killed by them.
After an introduction where one of the creators talks about Joel's actor constantly dropping his gun and asking Marlene's actress to improvise, you expect an improvised alternate ending where Joel screws up, drops the gun and gets him and Ellie killed. Instead he picks up the gun perfectly, only for Marlene to break out into broadway singing. Followed by Joel singing right back. The entire scene continues this way until the end.
Naughty Dog getting pissed when a magazine edited Ellie off of the cover. They were brutally honest about how many websites and magazines wanted to ignore Ellie because of the "Girls aren't gamers," routine, and seeing a developer not take stuff like this lying down is very awesome.
The infected and the hunters fighting each other in the last chapter. After so many encounters with them and the difficulties they give Joel and Ellie throughout the main game, it is oddly satisfying to be able to sic the infected onto hunters and watch the havoc that unfolds.