I like a lot of them, but let's see:
RBY: Gym Leader Battle Theme, Rt. 3 Theme, Mt. Moon Theme
FRLG: Same plus Sevii Island Route Theme (Rt. 42 Remix)
GSC: Rival Battle Theme, Johto Trainer Battle Theme, Johto Gym Leader Battle Theme, Dark Cave Theme, Team Rocket Battle Theme, Lighthouse Theme, Battle Tower Theme, Rt. 42 Theme, Champion Battle Theme, Kanto Wild Pokemon Battle Theme, Rt. 2 Theme (Viridian Forest Theme in HGSS)
HGSS: Same plus Rt. 47 Theme, Frontier Brain Battle Theme, Kanto Gym Leader Battle Theme
RSE: Rt. 104 Theme, Team Magma/Aqua Battle Theme, Slateport City Theme, Surfing Theme, Rt. 123 Theme, Underwater Theme, Victory Road Theme, Elite 4 Battle Theme
DPPt: Rt. 203 Theme, Gym Leader Battle Theme, Rt. 205 Theme, Team Galactic Battle Theme, Eterna Forest Theme, Rt. 225 Theme
BW: Wild Pokemon Battle Theme (BW2 only), Dreamyard Theme, Unova Gym Leader Battle Theme (the tune itself is really good, although I prefer BW2's), Gym Leader's Final Pokemon Theme (BW1 only. BW2's would be better were it not for the part at the beginning where it starts to sound too fast and then instantly slows down. Sounds like they messed it up and never got to correct it.), Team Plasma Battle Theme (again, both are good but BW2's is better), Skyarrow Bridge Theme, Bicycle Theme, Mistralton City Theme, Opelucid City Theme (Black), Victory Road Theme, Elite 4 Battle Theme, Lacunosa Town Theme, Undella Town Theme (Summer. IDK why they don't play it in Spring and Autumn, the Winter theme sucks), BW2 Rival Theme, Corless Battle Theme, Kanto Gym Leader Battle Theme (much improved and I like the retro sound of it), Hoenn Gym Leader Battle Theme, Sinnoh Gym Leader Battle Theme