In Super Robot Wars Alpha 3, the moment belongs to Shinji Ikari again. When the events of End of Evangelion play out, we get to the point where humanity is melting into goo, but instead of going screamingly insane, Shinji gets royally pissed off, marches down to Terminal Dogma and gives his father a piece of his mind. And by "piece of his mind", it means a "robot-sized katana to the face".
The whole level is pretty much a Crowning Moment of Awesome for the Alpha Numbers (protagonist group in the Alpha games), as they're effectively kickingBright Slapping the crap out of the merged Shinji/Eva Unit-01/MP Evas + Tree of Life, also known as God. This is while, by all rights, they ought to be melting into LCL, but they're just too damn Hotblooded to turn into goo.
After watching End of Evangelion and seeing how nigh indestructible and horrific the MP Evas were, who doesn't get satisfaction out of seeing them in a SRW game get utterly ripped to shreds by Mazinkaiser's Fire Blaster, Shin Getter's Shin Spark, SRX's Buster Cannon, GaoGaiGar's Goldion Hammer, Sanger's Zankantou etc.
In Super Robot Wars Alpha, the Third Angel is making short work of Neo-Tokyo 3 when a man in a snappy suit and a cigar steps out, and manages to fight the Godzilla-sized monster to a standstill with his bare hands. That man is Alberto the Shockwave.
Later, when fighting a different Angel, the Victory Gundam battleship Reinforce Jr. actually manages to kill it, leaving its captain stunned that it worked and everyone else wondering what the hell just happened.
For the record, only the Evangelion people and the captain himself are truly surprised. Everyone else just puts another notch onto the leaderboard, under Bright Noah.
From the second game, Ibis has an amazing one, when a major villain from Mobile Suit Gundam strafes the party with his exceptionally powerful and large Mobile Armor...and then proceeds to get his ass kicked by her when she appears in her transforming fighter and strafes the hell out of his Mobile Armor.
Hell, she has a lot more. Ibis going through massive Character Development right before her Mid-Season Upgrade (which consists of hefty stat boosts to her and her mech) by gathering up her Heroic Resolve. Up till that point, she has been suffering from truly low self-esteem from her past. Her managing to get over the past and then pulling off the Maneuver Gr AMX, the same maneuver that caused her so much hell, is this and a Crowning Moment of Heartwarming.
Musashi's Back-from-the-dead moment in Super Robot Wars Alpha 3, wherein he finds a way, depite being dead to reactivate Shin Getter Robo when it was obvious that the Getter crew needed it.
Super Robot Wars Alpha 2 also gave Musashi an epic moment. The Getter team is bound along with a set of hostages, and the villains are threatening to kill them should the Alpha Numbers approach. Musashi approaches in Black Getter and causes enough trouble for the Dinosaur Empire's emperor, Goll, to come out and deal with him personally. Undeterred, Musashi then performs his classic Daisetsuzan-Oroshi on Goll and throws him far away from the hostages. Declaring he's won, Gaogaigar then arrives with the Dividing Driver to separate the fight from the hostages, leaving the Alpha Numbers free to give Goll a righteous smackdown.
The opening of SRW Alpha 3. The entire thing is a jaw dropping spectacle of the Alpha numbers taking on an invading army. What really sold it for me was at the end when they manage to break on through to the other side, only to find themselves overwhelmingly outnumbered, to the point that you can barely see the background for all the enemies flying in it. All of the Alpha's look around in disbelief, until the camera zooms in on Mazinger Z. Which clenches its fist and charges at the enemy full tilt, inspiring the other Alphas to follow suit. The only thing that could make it more awesome was if JAM Project was rocking out a song while it happened.
In Super Robot Wars Alpha 3, following the Tear Jerker ending of GaoGaiGar FINAL, all of the Alpha numbers are trapped, apparently forever, in an interdimensional void, with only enough power to send two small children back to Earth. They're not even going to bring back help - none of the team has any hope of that - just to tell their story to the people they saved. To make matters worse, a villain with the ability to teleport into and out of the void at will has decided to put them out of their misery. Right when everything looks positively doomed, a beam of energy appears out of nowhere, and the pocket dimension they're in literally shatters, revealing a newly rebuilt and upgraded form of the series' flagship robot: SRX Altered Banpreios, which proceeds to load its traditional pilot (who was stranded with the other playable characters) on board and kick a truly epic amount of ass.
In the same game, but in Touma's path, the debut of his Super Robot RaiOh's upgraded form, the DaiRaiOh, singlehandedly destroys one hundred enemy mecha in a single battle.
Being an Expy of Kamen Rider, Touma gets lots of these. To wit, Rai Oh's first appearance is probably the manliest of the originals, then he gets Rai Oh's strongest attack, then he upgrades to Dai Rai Oh, where we get the above, then Dai Rai Oh gets Jinrai, which is basically a Rider Kick! performed with a Humongous Mecha, then he kicks the Big Bad into oblivion in the name of love! Notable also in that he's the only character who gets to do the last one, alongside Sanger.
In Super Robot Wars Alpha Gaiden, after the group is sent to the future, Sayaka and Musashi are MIA for a long while. It's finally revealed they are being held hostage by Archduke Gorgon, at which point he desires to use them as human shields. Banjou Haran from Daitarn 3 coldly and honestly declares he doesn't care how many people he'll have to kill, he won't let Gorgon live in this world anymore. His delivery is so bitter and cold Gorgon backs down and hands over Sayaka, Musashi and Daitarn's support crew, no strings attached. Utterly amazing.
While we're on a Mazinger note, Space Route Mission 36 (Shin Getter Robo, Stolen!): Kouji Kabuto dies in lava convinces the Eisia excavation team to escape as part of his plan...then reveals to Gorgon that the plan's entirety was them escaping and him acting as their shield. Cue Bolivian Army Ending...of the first half. Then Tetsuya Rocket Slaps him back to reason after freeing him from a Mechasaurus horde, and Mazinkaiser ensues.
In the Super Robot Wars Alpha 3 manga, after the heroes defeat the Big Bad, they're confronted by Son Ganlong. To defeat him, the Ide calls in all the rest of the heroes from the three previous games that didn't make it into the last one. This results in the largest Giant Robot beatdowns in fictional history. Up to, and including, Two Sanger Zonvolts.
Similarly, the Super Robot Wars Z manga has a story where The Edel Bernal sets Zeuth up to battle...the Alpha Numbers (circa Alpha Gaiden). This includes Mirror Match moments between ∀ Gundam and Gundam X, as well as having the Zeuth versions of Kouji Kabuto, and the Getter Team face off against their Alpha counterparts in Mazinkaiser and Shin Getter.
Especially of note is where Sanger's Thrudgelmir stops the Mugen Punch effortlessly with one hand.
In a Super Robot Wars Alpha Gaiden manga, it depicts the first part of the raid on the Earth Cradle; the part with Sanger and his Thrudgelmir. While the whole freaking battle is insanely awesome (this is Sanger), the one scene that takes the freaking cake is when Sanger has lost his Zankantou and the Thrudgelmir's arms. Mazinkaiser goes up to the Thrudgelmir to finish it off. What does Sanger do? He fucking HEADBUTTS Kaiser's head with the Thrudgelmir's horn. This maims Mazinkaiser's head off (barely missing Kouji's piloting block). It's a badass moment for both men involved. Mostly because while Sanger's slamming the horn into Mazinkaiser's pilder, Kouji is driving a Turbo Smasher Punch through Thrud's chest. AND NEITHER OF THEM STOP until both have smashed through their targets. Conclusion: Thrudgelmir with a huge hole in its torso, and Mazin Kaiser minus most of the pilder (and a very lucky Kouji).
Finally, you'd think that losing both arms and one of his Zankantous would put a damper on Sanger's ability to fight, right? Wrong. Being Sanger Fucking Zombolt, he then proceeds to conjure up his second Zankantou and wield it USING THE THRUDGELMIR'S TEETH.
As a testament to how insanely badass this fight was, the two most iconic attacks from it (Thrudgelmir's headbutting Mazinkaiser, and its growing the Zankantou to insane proportions and trying to take out the Alphas in a single swing) filtered back down into Original Generations.
In an early mission in Super Robot Wars Alpha Gaiden, in a pre-battle dialogue with Shu (who is in Neo-Granzon), at the end of which, with his usual cold seriousness, Heero states that the Zero System had shown him Shu's death.
In a Super Robot Wars Alpha Gaiden doujin, Jiron Amos takes control of the Boss Borot, and beats the crap of of a Bergelmir. What makes it even more cool is that to do this, he rips off the Borot's head, clenches it in one of the Borot's fists, and uses this not only for extra damage, but also to extend his punch range just long enough to freaking decapitate the Bergelmir. In short, Jiron Amos was channeling Tengen Toppa Gurren Lagann before it even existed!
The head-removal not only allowed for this, but let them dodge the Six Slaves attacks the Bergelmir uses "BOSS BOROT IS A MAN!"
Mazinkaiser / Shin Getter Robo scenario from Super Robot Wars Alpha Gaiden. While one route involves Kouji and company going toe-to-toe with a General Bat-piloted Shin Getter Robo to block a Stoner Sunshine, the other route was more epic. Namely, the Getter Team decides to go balls to the wall, and tanks the Stoner Sunshine with Getter G, using the energy to Shine Spark General Bat into submission.
'SRW @3'. During the GaoGaiGar Final storyline, everybody was under the influence of the 11 Lords of Sol's chemicals, causing them to feel relaxed to the point where they don't care about anything, even if Guy is getting his ass handed to him by Palpelapa(or however you spell it). Some people were immune to this though, the GGG mechs (who were switched off), Hiroshi Jeeg (who's a cyborg), Rei (who's.....an emotionless clone I guess) and the Virtual On guys (fourth wall breakers and maybe robots themselves). But one person was not only immune to these chemicals but actually manages to get the rest of the group to snap out it.....with his rock music! His name? Nekki Basara of 'Macross 7'! Why could he resist the chemical? Uh....because he's too hotblooded I guess.
Actually, Basara resisting the stuff may be because he has the Anima Spiritia. Depending on your perspective, that might as well translate into "too Hot-Blooded."
Basara gets another moment of awesome during the Information High level. Sharon Apple had already screwed over your team by effectively nullifying and locking all unit abilities and seishins. After barely killing a few Ghost X-9's, he shows up, plays "Holy Lonely Light", and suddenly your team is charged with so much Hot Blood the Battle 7 is free from Sharon Apple and ZAFT's control, and you team is back to normal, and much Bad Ass ensues.
General Bat gets his in Super Robot Wars Alpha Gaiden by fighting the Preventers/Irregulars in Shin Getter Robo, despite the fact even sitting in the pilot seat is slowly killing him despite the use of a device to lessen the getter rays effects on him but shin getter still emits so much getter energy that it is still harming him, but he doesn't give a shit as long as he gets to take the Getter Team with him, and manages to survive point blank getter ray poisoning afterwards so he can make a defiant last stand in front of Machineland when you have to fight him and Emperor Gore, pretty much establishing himself as insanelydeterminedbadass.
Speaking of moments of awesome, theres one person in the entire cast of Super Robot Wars Alpha Gaiden that has possibly the most awesome moments in the entirety of Alpha Gaiden manga, rivalling Sanger AND Jiron listed above AND one of the best contender for the best in the whole franchise. That mans name ? Tetsuya Tsurugi from Great Mazinger. Its a story depicting the prequel of Alpha Gaiden serving as the moment before Egret Fehu does his job at the Earth Cradle. What does Tetsuya do ? Oppening with the classic Big Damn Heroes Thunder Break to save the crippled base defense line of Gespenst and Valkyrie Squad, then, after making a Badass Boast that he dont care about anything, his job is to give a trashing to the enemy, he singlehandedly handles a whole Army of Mycenian Dragoon Squad resulting in a cracked and crippled Great. Then Ryuuma Shogun come only to get handled by a Thunder Break and a point blank all or nothing stab with Mass produced Photonic Beam Saber with a little help from Venus A.
This feat is so awesome that SANGER ZONVOLT himself stares at his prowess in such an expression that signifies fear. You read it right. Sanger motherfucking Zonvolt himself FEARED Tetsuya Tsurugi.
To quote what Egret Fehu said :
Egret Fehu: Right, just like all of you. One born raised for the sake of fighting... Humanity's own battle beast...
Egret Fehu: Maybe he represents the soldier people have sought to obtain up until now...
Delivering the final blow on Keiser Elphes in Alpha 3 is made a whole lot more sweeter depending on the character you choose and what attacks you deliver. For instance, using Shin Getter Robo's Shin Shine Spark ends with Ryouma telling Keiser "Now behold! The true power of the Getter!" before perform an Open Get while using Genesic GaoGaiGar's Goldion Crusher on him has Guy shouting "Keiser Elphes! HIKARI NI NARE!"
And previously, via a dialogue, the Ideon crews, led by Cosmo, finally managed to state out something that's impossible from the home series: Instead of being disgusted at humanity at war, Ide & Ideon chose humans and Earth over Keisar Ephes, satisfied that there are people like the Alpha Numbers, fighting bravely to protect everyone from wars.
In the Alpha 3 version of the final battle of Mobile Suit Gundam SEED, Rau le Creuset, in his final moments, goes off on his tirade of Humans Are the Real Monsters justifying his actions. Usually, Kira Yamato would just fall into Heroic BSOD. Here? No. The Alpha Numbers proceed to tell that Rau is just bullshitting and throwing a tantrum like a childish egomaniac and proceeds to hand him the truth: He's the guy who needs to just go die if he hated the world so much, ESPECIALLY after his shit tons of crimes, even Kira eventually picks up the mood (and carries over to subsequent SEED appearances in SRW).