Daisy, Rand's mother, sacrificing herself to save Rand from a deathtrap.
Nina's little sister, Mina, sacrificing her humanity to become The Great Bird (sparing Nina from making the sacrifice herself).
The music, Mina's final words, everything about it...the fact that, not too long afterwards, you lose her for the rest of the game was just the final twist of the knife: short of getting you to one little location, Mina's sacrifice ends up being for nothing. Capcom, you bastards.
NPC rebel leader Tiga charging the Big Bad (who turns out to be the game's true Dragon) Habaraku, to save the woman he (just realized) he loves. Only to have Habaraku brutally (especially for a sprite based RPG) murder them both. ( The shot of a broken Tiga crawling towards Claris' body, just to have Habaraku vaporize them both with lightning WILL HAUNT YOU.)...
All the while, the bloodthirsty brainwashed audience is watching and cheering.
The Dragon Rock at the edge of the city revealing itself to be Ryu's mother, just in time for her to give up her life in order to clear the way for Ryu and company to track down the true Big Bad. (The seal could only be broken at the cost of the life of a member of the Dragon Clan)
The bad ending shows what happens if Ryu prevents Valerie from sacrificing herself. He finally gets to meet his mother and live with her for several years. Oh, and the Big Bad gets strong enough to break the seal and slaughter everything. He's the last thing you see before resetting the game.
The "default" ending (the one you get if you beat the Big Bad, but don't complete a certain set of subquests) has Ryu taking his mother's place as living seal to the demon's realm.
Oh God, so many. The Church of St. Eva sequence is good for about three or four alone.