One of my favorite moments: The first time I ventured into the murky water in the Flooded Forest of Monster Hunter 3 Ultimate to kill the Royal Ludroth. It was so dark and I did not like water at that time.
Another good moment was a deceptive mission to collect monster guts. Very easy. You can get them from fish. Then I got attacked by a huge creature and barely escaped to complete the mission. All under water when I could barely swim.
Favorite moment: I just beat the monster in Monster Hunter 3 Ultimate that I could never beat before! First time! I can now face new monsters and have a whole list of new quests and equipment open! ^_^
~Pretty much any Master Sword cutscene in the Zelda franchise ~The "We believe in you, Mario" cutscene right before the final Shadow Queen phase in PMTTYD. ~The Dark Knight Cecil battle in FFIV. ~Somehow managing to 100% the original Pikmin during my very first playthrough of it. ~The credits for the Game Boy Advance version of Legend of Spyro: Eternal Night. (It made me cry a bit... I don't know why.) ~Getting the third gear in Drill Dozer. ~Shadow kicking Silver in Sonic 06. ~Dimitri boss fight in Castlevaina dawn of sorrow.
~Pretty much any Master Sword cutscene in the Zelda franchise ~The "We believe in you, Mario" cutscene right before the final Shadow Queen phase in PMTTYD. ~The Dark Knight Cecil battle in FFIV. ~Somehow managing to 100% the original Pikmin during my very first playthrough of it. ~The credits for the Game Boy Advance version of Legend of Spyro: Eternal Night. (It made me cry a bit... I don't know why.) ~Getting the third gear in Drill Dozer. ~Shadow kicking Silver in Sonic 06. ~Dimitri boss fight in Castlevaina dawn of sorrow.
I found the end to Castlevania Lords of Shadow: Mirror of Fate for the 3DS to be absolutely heartbreaking. You should watch it sometime if you have not, but it has some spoilers.
That scene from Thousand-Year Door is also one of mine. I was in awe as all the past characters gave Mario strength.