While there are plenty of awesome moments in Peace Walker, one of the most memorable is the entirety of the "Get to the Control Tower" mission, particularly when played in single player. The climax of the mission is when the player encounters their final obstacle; a squad of commandos and a chopper, all of whose sights are centred directly on you. Making it even more intense is that the player is likely running quite short on ammo, and the building the player enters through is promptly blown apart by the chopper, taking away most of the player's cover. If that's not enough, the main vocal theme of the game, Heavens Divide, begins playing in the background. It is probably one of the most intense and awesome moments of the game, possibly even of the entire Metal Gear series, especially when the player finally takes down the chopper.
Taking down Metal Gears is always awesome, but taking down Metal Gear Zeke to Koi no Yokushiryoku, instead of the typical electronic music was pretty damned sweet.
The real kicker is going outside at the start, even though Miller says it's suicide, and getting on the mounted machine gun. YOU CAN'T GET HIT USING IT. Time to go Rambo.
And to make it even better, the mission ends with things getting tight for Snake, up 'til when the Sanadistas arrive, gunning down all the enemies in one of the best Big Damn Heroes moments in the whole series. Cue to Amanda finally being recognized as "Comandante", and after she hugs Big Boss, everyone starts cheering for him. It's such a moment of glory.
The QTE at the end of Infiltrate the Underground Base. The prompts are so fast it's borderline impossible to avoid losing (and continuing to the next mission), but Big Boss' CQC Foe-Tossing Charge (not to mention stealing Strangelove's ID card to escape later on upon completion) is totally worth it.