Ohhh, just so many to choose from! I grew up with Pokemon Diamond, so I'd really like to say I like every track in the gen 4 games. Other tunes I really enjoy (that aren't in gen 4):
- Zinnia's theme
- Lance/Red's theme
- Geosenge Town
- Bittercold/Dark Matter (Pokemon Mystery Dungeon GTI and Pokemon Super Mystery Dungeon)
- Mount Lanakila
- Route 10
Those are just a few that I could think off the top of my head, but I pretty much enjoy 99% of the music that Game Freak puts into their Pokemon games. The only theme that I've hated so far is probably the gym leader theme in Pokemon X and Y. I'd also hate the Elite Four theme in Pokemon Sun and Moon, but I've grown to like it since I heard the SSBU remix of it.
I used to make Pokemon Music Remixes. Here's my channel:
Overall I'd say the PMD franchise soundtracks as a collective are my favorite. Even the "black sheep" of the quartet has some awesome tracks in it. Battle against the Bittercold? So good.
But there are some really good tracks in the main games too. All the Team Skull themes I love as well as the Aether Foundation workers. Ho-oh's battle theme in HGSS and Giratina's in Platinum are also big favorites of mine. And I love all the iterations of the Vs Maxie/Archie theme they've done.
I wouldn't call it my "favorite" song in the franchise, but the Lavander Town theme is something special to me. It's gone through so many different versions, all of which have something a little unique to each of them. From Gen 1's teeth chattering creepiness, to Gen 4's more brighter take on the song. Getting to hear so many different versions of it really makes it stick out in my mind.
Call me an oldhead but it's the Battle Red music in Gold, Silver and Crystal.
Track Number 2 of my debut Mixtape, Venting Session Vol.1: What's it like - https://youtu.be/Qxs6shEpHIo
A lot of emotions, thought and a bit of nostalgia went into the making of this particular track on the Mixtape.
I wish there was some kind of app where you could whistle or hum a tune and it would identify the song. I have a very particular melody in mind, but I just cannot remember which game it's from, let alone which area!
Those are my favorite pieces of music per region in the core series games:
Kanto - Route 1 (RGBY)
Johto - Goldenrod City (HGSS)
Hoenn - Surf theme (RSE)
Sinnoh - Route 210 (For some reason, I think it would be a great ringtone)
Unova - Route 1
Kalos - Aquacorde Town, probably
Alola - Route 1
Gen I Team Rocket's Hideout - really like the sound of it, brings in a sense of danger
Gen II I have two faves here, couldn't narrow it down to one since it's such a good soundtrack...
Trainer Challenge Theme 1 - love the feel of this one, action/adventure... and Rocket Tower Takeover, it feels a lot like the anime here, and it makes me grin from ear to ear
Gen III Wild Pokémon Battle ! - like this one in terms of bringing some excitement into the battles
Gen IV Television Channel - just like the pleasantness of this theme
Gen V Unwavering Emotions - first song in the series to almost bring tears to my eyes, so emotional and well composed
Gen VI Pokemon X & Y Wild Pokemon Battle Theme - one of my favorite battle themes, just really well done
Gen VII Battle! Wild Pokemon! - thought this one was pretty good
Side games (putting them here) - from Pokémon Colosseum (love the entire OST to be honest) - Normal Battle - love this theme, it's fun to listen to; from Pokémon Trading Card Game - Club Leader Duel - love the intenseness of this theme; from Pokémon Mystery Dungeon: Blue Rescue Dungeon - Tiny Woods - just really like this theme, nice and light