Super Metroid was a terrifying game for me as a child. From Crocomire, to Ridley, Super Metroid was full of epic boss fights. But fighting Mother Brain was the best fight. What started off as an homage to the original Metroid fight turned out to be one of the most intense battles I have ever experienced.
After destroying Mother Brain (or so you thought) she rises up as a monstrous beast of steel and flesh. Mother Brain then promptly decides to kick in Samus's face, until the last metroid shows up and saves Samus, sacrificing itself to get our hero god-like power to finally defeat Mother Brain. Don't forget about the three minute timer after the fight. I hope you have your Nike's on, because you're going to be running for your life.