I'd like something like the Albedo/Jr. relationship in Xenosaga. Albedo starts out as this crazy lunatic with an awesome laugh and then by the third game when you see that he and Jr. still love each other and it was just

Or you could go the Suikoden route and have someone betray you. But have them do it AFTER you defeat who you think the main villain is. Then they're all like "SURPRISE!!" and you're all shocked and stuff