Wind Waker soundtrack beats Ocarina, sorry guys. Still the best Zelda soundtrack.
Can't speak for all-time greatest. I suppose I'd say either Mario Galaxy or Xenoblade had the best OST on Wii. Picking a Smash Bros game feels like cheating, especially for Brawl and 4 where half the tracks are ripped directly from the source material rather than remixed (not that I mind).
Best OST on 3DS is still Kid Icarus in my opinion, but dammit does Bravely Default make this a hard choice. For DS I'd probably go with a Pokemon game. Black 2/White 2, I suppose. GameBoy - Link's Awakening, GBC - Oracle of Ages, GBA - maybe one of the many Mega Man games?
For the NES I'll go with Mega Man 2, for the SNES I'll pick F-Zero, N64 Ocarina, GameCube Wind Waker. Best soundtrack on Wii U so far is Shovel Knight.
Journey really deserved its Grammy nod, that music is fantastic.