I love all of them really. I don't think I can choose just one or even a few. They were all unique and had amazing and memorable music. I guess I liked Gen 5's the least, though I must say Unova's Route 10 is fantastic. I had it on my old iPod shuffle, I loved it so very much.
For gen I and II, the 8 (16?) bit music was just perfection. To this day it really only holds nostalgia, but a special kind of nostalgia. I still love listening to the SS Anne music of Red/Blue/Yellow, and the National Park music of Gold/Silver/Crystal.
And then Gen 3. Oh my goodness. Those trumpets were so charismatic and signature of the generation. I miss it a lot. Firered and Leafgreen's music didn't stick out too much, probably because it was mostly all just updated remixes of old music I previously really grew attached to. Heartgold/Soulsilver was the same way, though I feel like they did better than Firered/Leafgreen.
For Diamond/Pearl/Platinum, the vibe I get from thinking back on its music is "dreary and solemn", which might sound bad but I have good memories with it. Those games overall had a pretty soft, easygoing, dignified sort of feel to them, which made them unique to other games, in my head.
For X & Y, it had some pretty amazing music, some of it is kiinda forgettable though. I enjoyed the champion's music a lot. And most other tunes were just very modern and catchy and just... work. You know?
It all just works. Pokemon does a pretty great job with music, all things considered. <3