I have already picked the music from the first season of Pokemon that I believed was the best. But because the Johto region reused a lot of the Kanto region's soundtrack, there won't be as much music on this list. Now here is my take on season 2, Johto region.
Pokemon Season 2-Johto Wild Pokemon Battle:I think this is the best wild encounter song in the series. It can make a Level 4 Pigey fighting a Level 3 Weedle epic.
Pokemon 2000-Harmony Disturbed (Expanded):"Disturb not the harmony of Fire,Ice, or Lightning lest these three titans wreck destruction upon the world in which they clash. Though the water`s Great Guardian shall arise to quell the fighting alone its song will fail. Thus Earth will turn to Ash." This song opens with a beautiful ocarina, then changes to a darker tone. Played in the beginning of Pokemon 2000, this song greatly sets the mood for the movie.
Pokemon 2000-The Legend Comes to Life: From Pokemon 2000, this song brings images of Pokemons and humans coexisting without harm. The beginning is introduced with an ocarina, which makes the song sounds more mystical. As the song progresses into the orcstra, I am reminded of the girl playing the ocarina, and the river floating above her, as the Pokemons and people become amazed of the scene. Lastly, the song comes back to the ocarina as if Ash's adventures will become legends.