Even though pretty much all of my Pokemon favorites tend to be from Gen 1, I just can't help but think that my favorite Pokemon song is Azalea Town's theme from the Johto games. I'm a huge fan of the series as a whole (except Gen 5), and to me, Azalea Town's theme IS Johto. It is what I think of whenever Gold, Silver, HG, SS, or, most importantly, Crystal come to mind. I first played these games, like Gen 1, when I was four. I'm so happy I did, and Azalea Town's theme always puts a grin on my face.
GBC games version: http://www.youtube.com/watch?v=SQ4JfSoNuYk HG/SS version: http://www.youtube.com/watch?v=9z59kCAkNp4
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