After beating Pokemon White, I'd have to say the Ghetis final battle theme is quite amazing, as is the music that plays every time a Gym Leader/Elite Four member/Important character gets down to a sliver of health on their final Pokemon. Both are very well made themes, of which there are many in the entirety of Nintendo's many storied game series.
It's my job to help the next generation, and set a good example for them. And for that I'll gladly lay down my life.
Diamond: I liked the relaxing theme of the Resort Area.
HeartGold: I liked the theme when traveling up some mountain before you get to battle the first elite four and get to travel to the other side. It's music was quite energizing and bold. I also like the theme inside the Poketheon. Its was energetic and powerful which easily matched the competitive spirit the you feel when you enter the Poketheon. The bright lights inside the Poketheon were awesome because they illuminated the arena and made you feel excited and energized as well.