Skies of Arcadia Legends (Gamecube):
I find it a nice touch that in the ending credits you can see, in text, what happened to each of the crew members of the Dolphinus that you recruited during the game. Some ended up together, others returned to their places and have stories to tell and experiences. I like that touch... Oh and seeing Cupil with an eye patch made me chuckle, lol.
Terranigma(SNES):
After you defeat Dark Gaia, your creator, your existence will be no more. Light Gaia grants you a wish to see your family and friends one more time for one day, like before your journey even began. Then you dreamed you become a bird and fly away as you see the world advancing thanks to your efforts to save it. It ended as the Elle from the light world opens the door of her home.... Damn I wanted to see more TT_TT. Did he become human again to see her? I wanna know
Tales of Phantasia(SNES/GBA):
Never expected to feel bad that I beat the last boss in the game, Dhaos.
Grandia(PS1):
Justin and Feena end up having adventures together. After a few years, a grown up Sue goes to the port to welcome our two heroes only to be seen by Justin and Feena's kids