I can't fucking choose one from one generation. Have several from all of them.
The Rival Appears music in Red/Blue/Green is one of my favorites. (The violin remix of this in Origins made me orgasm)
http://www.youtube.com/watch?v=EjA4SgVDmh4There's also the champion battle music, which is amazing.
http://www.youtube.com/watch?v=ptXXzQ_dXwgThen of course there's Lance/Red battle theme from Gold/Silver/Crystal
http://www.youtube.com/watch?v=hAOGtJLMHlcThe elite four battle theme from Ruby/Sapphire/Emerald
http://www.youtube.com/watch?v=VBepEXguNKgFuck you if you don't like the Gym Battle Theme from Ruby/Sapphire/Emerald
http://www.youtube.com/watch?v=E76zZ-lH8k8Piano before Cynthia is one of the best from Diamond/Pearl/Platinum
http://www.youtube.com/watch?v=VBkHuCAci1oThe other best is Cynthia's theme
http://www.youtube.com/watch?v=hJ4OUOQjqgkBlack/White has so much good music. Ghestis theme
http://www.youtube.com/watch?v=bLdjl65jAB8Elite Four theme
http://www.youtube.com/watch?v=XnJwd9zrjiAN's theme
http://www.youtube.com/watch?v=8s6IkFafrK4Route 10
http://www.youtube.com/watch?v=465uaHc-r6ATower of Heaven
http://www.youtube.com/watch?v=V4u6ht7TtVoPlasma battle theme
http://www.youtube.com/watch?v=cp3FtEaV7tQI think Gen 5 has the best music out of all the games. I'm not saying that music from the other generations is bad, because there's some amazing pieces, but Gen 5 is just full of fantastic music.
Then the gym leader music from B/W 2
http://www.youtube.com/watch?v=_VfGig0R83kI didn't get to play much of black 2 because my DS broke, so I didn't get to hear much of the music. 
