GSC has the best music, the best Pokémon, the best story, the best Rival (Silver), the best final boss ever (Red)...You see that team in my signature? That's my main fighting squad in Silver Version, which is by far my favorite in my whole collection!
As far as music goes, I particularly like the Rival's appearance theme, the Rival's battle theme (which I have affectionately dubbed "Preemptive Strike"), the Lucky Number Show, Buena's Password, Indigo Plateau, and Lance/Red's battle theme (which I have affectionately dubbed "Ultimate Challenge!").
I do have one question about the music, and it isn't restricted to Generation II: Why does the Rival always have better theme music than the player?!
D/P is the best, I like the music from route 217(the route where you can evolve Eevee into Glaceon, my file is always saved there), and I like the music from the area in front of the battle tower(also in D/P). I shouldn't forget to mention the music in the ghost house and the music in the final battle of elite4.
Anyway, the music from GSC was good as well, but not better than D/P....
Personally, I prefer R/S/E and D/P to G/S/C's music. There are some G/S/C songs that are good. The Beasts, Lance, and the Ruins of Alph come to mind. They get stuck in my head, although not for long. A lot of the 3rd and 4th gen songs remain stuck in my head for a while.
The Elite Four in RSE was the best battle song out of them all, in my opinion. Veilstone city is also really nice.