My favorites from G/S/C include: Rocket Battle theme, Final Battle Theme, Goldenrod City, The lake of rage theme, and Blackthorn City theme.
I will have to admit that the Vermillion City theme is my number one favorite piece of music from a Pokemon game. It's just so catchy and energetic.
All of the music from the first two gens are amazing though and blow all of the other games in the series out of the water in my opinion. All of the remakes and newer Pokemon games way overdo the music and make it sound way too clean. The 8 bit music focuses on the melody and doesn't include all of the flashy stuff that makes the new music boring. The 8 bit music is also much gritter sounding, which is great for me since I love metal music.
Goldenrod City music is really very very incredible. When i listen it, i remember when i am 5 years old.