Saving all the cryotrays in the third mission. These are the last remnants of your entire civilization. One hundred thousand souls are crammed into each tray. You can hear the undertones of heartbreak turning to anger in the bridge officers voice as he issues the mission orders.
Bridge Officer: The cryotrays are under attack. Defend them. ... These ships are different than the ones we encountered at the Khar-Selim. It is likely they were involved in the destruction of Kharak. Capture at least one vessel for interrogation, and destroy the rest.
From the end of that same mission, just five words: Subject did not survive interrogation.
The final mission, all of it. The enemy managed to disable Fleet Command and you have no more warnings about ship losses, construction and enemy attacks (thus slowing you up), the full might of The Empire is upon you, the only help you have is what few ships the rebellion managed to scrape up and bring there... And you kick back the full might of The Empire, kill the one who ordered the genocide of your people and finally return to your true home.
The crowning moment in that mission comes as a constant flow of enemy reinforcements begins to overwhelm you... until the most recent arrivals turn out to be a fleet of rebels who immediately spearhead a charge right through the Emperor's forces, dying while clearing a path for your own final attack. Barber's Adagio for Strings plays through it all - the same song that plays when the Mothership was first launched, and when discovering that your world had been firebombed into lifelessness in the third mission. Retribution was never so awesome.
The Bentusi in Mission 5 are being taken over by the Beast. Shocked, overwhelmed, and horrified, and knowing that there is no way for them to survive. And then....
The Bentusi are so scared of the Beast that they're trying to flee the galaxy. Problem is, the Somtaaw need their help to get the Kuun-Lan's Siege Cannon operational. To get their point across, the Somtaaw destroy the hyperspace gate the Bentusi were trying to escape through... which results in seven Bentusi ships coming out of hyperspace and descending upon the Somtaaw fleet into a Curbstomp Battle of epic proportions. The Kuun-Lan's captain hurls insults at the Bentusi while battling them, calling them the galaxy's biggest hypocrites for running away and letting everyone be consumed by the Beast while still calling themselves the good guys. And the Bentusi get so ashamed of themselves they actually back down from the fight. The whole thing can be seen here.
Just for reference: no one in recorded history ever engaged a Bentusi tradeship and lived to tell the tale. This guy did.
Captain: Aren't you...? Look around! Look what you've done to our fleet! All because we dared to stand in your way! Look at yourselves: the aloof and mighty Bentusi! Slaughtering the people who ask for your help! You're worse than the Beast!! AT LEAST THE BEAST DOESN'T PRETEND TO BE RIGHTEOUS!!!
The end of the next mission, which is just before the final one, also has an excellent delivery of a very simple line.
The start of the final mission. Throughout the game, Fleet Command always identifies the Kuun-Lan as what it is: basically a huge refinery and construction ship. Except throughout the game you have been slowly upgrading bits of it, improving its defenses and strapping a huge cannon to the side of it. Then the final mission comes:
Fleet Command: Republican Fleet, this is the Kiith Somtaaw Warship Kuun-Lan. Will try to send help while you regroup.
It's about then that you realise that you've pretty much rebuilt the lumbering mining ship into an immensely powerful battleship...
The last-minute return of the Mothership/Sajuuk Fleet to Hiigaran space in the final mission of Homeworld 2. You can see the last remnants of the Hiigaran defense fleet who stayed behind to protect the planet getting chewed up by a huge Vagyr onslaught. They've been pushed to the final defensive line, directly in orbit over Hiigara. Then the screen cuts to your fleet jumping in. Cue Karan, calmly announcing the arrival of a legend and the total reversal of a Curb-Stomp Battle: