I have too many favourites. A lot of Pokemon music is good, but I guess my top 5 would be:
Unova Gym Leader Theme BW2 Kanto Champion Theme Colress Battle Theme Lilycove City FRLG Cerulean City
But really, I like all of the Gym Leader, Champion, Wild and Trainer battle themes a lot. Many town and route music also appeal to me quite a bit. The only music I dislike from a main Pokemon game I can think of right now is Eterna City. I just don't like the style it's in.
If life gives you lemons, sell 'em to Tom Nook. Black 2 FC: 0132-9980-0476 (Aki), 3DS FC: 5284-2520-2972