Donkey Kong Country 2 is my favorite video game soundtrack of all time. So that definitely takes the cake when speaking specifically about Nintendo as well.
If I made a top 5 list of Nintendo soundtracks it would probably be as follows (probably):
5: Super Mario Galaxy
4: Super Mario Galaxy 2
3: Donkey Kong Country
2: Super Mario RPG: Legend of the Seven Stars
1: Donkey Kong Country 2: Diddy' Kong Quest
Sure, not the most versatile list. But we're listing favorites here. I could name so many more great ones... Probably the notable runners-up would be Wind Waker, Tropical Freeze and Super Smash Bros. Brawl (which I only didn't list in the top 5 because a lot of it reuses music from other games' soundtracks, and I guess when making these lists I favor originators). If we're not just talking about games made specifically by Nintendo than also throw Secret of Mana and Banjo-Kazooie into my hat.