Well, I have a few, most are before/after a boss fight in the metroid prime trilogy.
Best: When you are fighting RUndas, one of your allies, corrupted by your archfoe, dark samus. It starts out as a fight against a dropship of space pirates, and just when you think it's over, this creepy music plays, then the middle of the arena erupts with ice and rundas leaps out of the middle, He crouches in an atttack form and you can see a shadow of his corrupted self. Then after the fight, He goes to kill you, but is so disoriented and injured, he accidentally impales himself on a giant icecicle.
Another is on the GFS Olympus. You're in the briefing room, when suddenly the commander stops, the entire ship goes into code red from an enemy attack. The commander throws down his fist "Damn! they'r targeting the planetary defense systems! all the other people run out of the room, and as you leave, it shows a view outside the bridge, suddenly, the ship nearest the Olympus is hit by a huge red beam. There is a huge explosion, as the ship splits in half. And as you get down to your ship, the scene outside looks like the battle at the beginning of Star Wars Episode III, and when you finally get to the hangar bay, a soldier is thrown from the second story window, and as you go to see if he survived, a huge berserker lord leaps out and begins to stalk you across the bridge. After you fight it, it stumbles off the platform, where it drifts into the vacuum of space, where it is hit by a fighter and both explode. After that, you fly down to the planet Norion , There is an even bigger battle, and the story soon unveils that a huge leviathin phazon seed is hurtling towards the planet, and it'll kill all the soldiers if you don't destroy it.
the third is the beginning of metroid prime. The space station is like a horror themed game and was very original when it first came out.
