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EDIT: In all honesty, probably Fei and Elly in Xenogears. It was just such a well fleshed out relationship and I love the jump from bitter enemies to basically discovering they're soulmates (and not just figuratively); not to mention they actually did the deed before the end of the game and it was handled very tastefully. Most Japanese games aren't even willing to show anything beyond a kiss. Blew my freakin' mind at age 14.