It also doesn't change what happens in the ending iirc.
When you say "special endings," are you looking for games where the player's actions can influence the outcome of the game's narrative, or are you after games with challenging "postgame" content?
It's a little bit of a stretch, but in Ragnarok, the number of Aesir who survive the final battle depends on how successful you were in completing your quests. Does that count?