Heero Yuy'sBig Damn Heroes moment in 3 (also arguably the only thing he exists in the game to do). When the Gekko is surrounded and has their escape path blocked off by at least 80 squadrons of enemy Mooks, Wing Zero pops up out of nowhere and wipes them all out like it's no big deal, then proceeds to hold off enemy reinforcements while the player handles the stage's boss.
Ruri: In light of current emergency, we'll take you up on that offer and beg your favor.
Heero: ...Mission Acknowleged.
3's rendition of final acts in Char's Counterattack is pretty awesome too- on one hand we have Earth Federation (including characters from other series integrated into the Earth A universe) and Neo Zeon soldiers alike being inspired to join Amuro's dangerous attempt to push Axis away from the gravity well of Earth A as having happened in the anime film; on the other we have characters from Earth B, who have no stake whatsoever in the safety of Earth A, promptly helping with the push alongside simply out of their determination to not have the devastations of 7th Space War repeated there, leading to a collective crowning moment of awesome for everyone involved.
The best part? Every single mecha pushing against Axis. And it works.
Mission 25 of ACE 3, the final Eureka Seven mission. It's the charge of Gekko, with everyone helping out and encouraging Renton to get the girl, while Sakura plays.
The final battle in 3: the player's fighting against Shin Getter Dragon, with two Earths in the background and Shinku as the BGM.
Quite possibly the only redeeming moment in the scrappy final Macross Frontier mission of R has Ranka Lee and Sheryl Nome singing along with nearly all of the mecha saluting, following Alto's example from the anime...except for the Strike Freedom and Zeta Gundam, as they're holding their own weapons in both hands.
After kicking the crap out of Big Bad Doctor Shiki's robot in the final mission of R, Autumn Four is about to arrest him (he reveals prior that his death will cause the ACE system to collapse and destroy the world, so killing him is out of question) when he threatens to fire Beldona Penetrator and subsequently send the heroes to a random unknown dimension. Shiki then proceeds to cackle on about he's won and the heroes are doomed... until Lelouch goes on to shut him up by Geassing him into witnessing an eternal nightmare. Pure and satisfying retribution.
as for how Lelouch could...... Doctor Shiki had his still-human brain placed inside Winter One; since Lelouch's Geass power can be transmitted via video signals (as shown during the Tokyo Uprising segment, near the end of the anime's Season One), having cameras for eyes doesn't at all protect Dr. Shiki against it.