I'm pretty sure Actraiser is on the VC, but that's an Enix and not a Square game (great series, too). Come to think of it, I don't know of any Square games that are on the Virtual Console, but then again I don't have a Wii.
Besides the Chrono Trigger remake attempts, I think there was an Aliens fangame attempt that got smashed a long time ago. Interestingly, that attempt, like CT:Resurrection, was going to use fan-made and not original resources if I remember correctly. Confuses the heck outta me -- you'd think the game companies would be more angry when people use ripped resources as opposed to self-generated resources. Maybe it's because the fan-made resources sometimes turn out better?