I'm sure its in here, but the National Park in HGSS is one of the best video game pieces of music there is.
And I know a lot of people don't like Gen 4 (Its my favorite as far as storyline and in game), but man, overall I think it had the best music of all of the games. Whoever wrote and recorded those tunes deserves a medal of some kind. Palkia, Giratina, Cynthia, nearly every route, Looker's theme is really cool, their use of piano was really well placed in this gen, and the music really added a lot to the game.
Also, the S.S. Anne theme is really good. I think its very appropriately composed, it fits really well.