Updated everything but #1 (though anyone who knows me should be able to work it out)
5 - Wii - Mario Kart Wii (Nintendo)
4 - VC - The Legend of Zelda: Majora's Mask (Nintendo)
3 - N64/VC - F-Zero X (Nintendo)
2 - Wii - Endless Ocean 2: Blue World (Nintendo)
I originally owned F-Zero X on the N64, and that was where I spent most of the play time. It is, I think, the only game I have ever bought twice. I now have it on the Virtual Console, though I have only spent 16 hours on that version (that is still the third most played of my VC games, only behind SM64 and LoZ:MM, neither of which I had played before getting them on VC)
The only other game I have played extensively on 2 consoles is LoZ:Ocarina of Time... which, as I mentioned earlier in the thread, I originally played and completed on my friends N64 but didn't own it until the GC version that came with my WindWaker pre order.