From D/P/P, one of my top favorites is the music in Sunyshore City. It felt perfect for a port town by the sea which is also the last stop before the Pokemon League. The melody and the instrumentation is great.
From Platinum, I liked most of the new music introduced, especially the Giratina Battle theme and the Frontier Brain battle theme. Those were both great battle themes that suited their situations perfectly. I was surprised the first time I battled Giratina as the music was just so intense. And then, when I reached the Frontier Brains, I hadn't expected them to be able to make a theme that was on the same level as the one in Emerald, but they succeeded with that.
Others I like from D/P/P are these: Route 201, Gym Leader Battle, Jubilife City, Canalave City, Pokemon League, Snowpoint City, Route 216/217, Route 225, Distortion World, Uxie/Mesprit/Azelf Battle, Credits, regular Trainer Battle Theme.
From HG/SS, my three top favorites are these:
Ho-Oh Battle theme. Another fantastic battle theme for a legendary. I definitely prefer it over Lugia's Battle theme because it suits the Pokemon and the situation better, it is relaxing yet uplifting and has a bit of energy into it.
Ecruteak City. This was a recreation of the original track which added a bit more mystery to it while keeping what made the original good. Probably the main reason Ecruteak is my favorite Johto city in HG/SS.
Cinnabar Island. I love everything about this. It took the original from the Kanto games and changed it so that it became perfect for what Cinnabar had become three years later. Sometimes I went to visit Cinnabar for no other reason than being able to hear this.
Some others I like from HG/SS: Cianwood City, Bell Tower, Route 47/48, Lavender Town, Hoenn Sound, Sinnoh Sound.