Chrono Trigger should be the template on how to do multiple endings. The 'true' ending had subtle differences you could make in it which were really cool and all of the alternate endings were amusing and tied into the point in the game that you beat it.

Also FFVI had a truly epic ending that was like 20 minutes long but it gave every character a moment and I loved that.

However, the best RPG ending was FFIX as had already been stated. You kind of knew what was coming but it still had the emotional impact. Then they gut punch you with the fate of Vivi...