Locke and Terra. When I first played, I was pretty sure they'd become a canon couple (before the entire Rachel segment) but I guess not. Not that Locke and Celes ever became a canon couple either.

Personally, I'm a little disturbed with pairings such as Freya x anyone who isn't a fellow rat, Vivi x anyone who isn't a fellow black mage (does Vivi even have a face...? he's just a black blob with a hat or something), and the like. It's a nice concept but if you really think about it... *scringe*