The obvious ones I can remember easily are:Castle Fantasia (+Renewal)
If you follow the path for freedom, you end up doing a chain of onslaught missions where the country's military is trying to kill your group before you desert and fleet by sea.
The difficulty goes way up (hardest in the whole game) and a special background song starts playing. It's the first and only voiced song in the game.
It's a really incredible experience as you fight the kingdom's oppression against terrible odds.
I've never felt as 'engaged' in a game's moment as this one
The song (if you consider ever playing the game, don't listen - keep the magic for that moment): http://www.youtube.com/watch?v=b7xqCWy-EW8Ar Tonelico 2
Using Replekia and then harmonic chain. POWER OVERWHELMING !!!http://www.youtube.com/watch?v=jt1ASvGnkVE#t=83Ever17
MIND = BLOWNTerranigma
The ending screen
I stood there for MINUTES just looking at it.Final Fantasy V
Gilgamesh turning traitor
I'm sad that now Gilgamesh is just a gag extra boss in recent FFs =(Chrono Trigger
Opening the path to Magus' castle (the Masamune)Star Ocean 3
The fight against Crossel.
I like the build-up to it, the fact that he is enormous and the awesome songhttps://www.youtube.com/watch?v=XoLLM72RKPA#t=114
Almost forgot!!!Zone of the Enders: The Second Runner
By far one of the best level out of any game.https://www.youtube.com/watch?v=c8tIjRDz0cA#t=355
+ boss https://www.youtube.com/watch?v=1Tjr2pvus6A