My favorites from each main series game:
RBY:
Route 1 - Catchy as hell, sets the stage for what was at the time a fun adventure, and still enjoyable to listen to today. Just about everything I could want in an early route theme.
GSC:
Dark Cave - If you're going to make a giant labyrinth of a cave, you may as well at least make the theme interesting. This tune is just that. I especially like the bass and chord progression.
RSE:
Bike Theme - This tune is exhilarating and pure ear-candy. A lot of songs from this generation and its remakes are, but this theme especially. I actually listen to it while I'm out cycling in real life from time to time.
FRLG:
Sevault Canyon - I like FRLG's remixes of various Johto songs on islands 4-7, and this theme is perfect when exploring the outlying areas on Six and Seven Island.
DP:
Route 225 - For as much as I've complained about things I dislike in Gen 4, I will say that the postgame is phenomenal. And this route theme is just another reason why.
Platinum:
Giratina Battle - Had to put this on here. My favorite legendary battle theme in the series and fits Giratina flawlessly.
HGSS:
Safari Zone Gate - HGSS had a ton of great new tracks to listen to that weren't in GSC, and I realize this isn't as popular a pick as Ho-Oh's battle or Route 47, but I just love the beat, melody, and instrumentation of this theme too much.
BW:
Icirrus City/
Route 10 - Can't pick one without the other, so I'm going with both. I love the jovial and free-spirited feel of the former, while the latter feels very regal and majestic (pretty fitting for the final stretch prior to Victory Road). They also have nearly the same instrumentation.
B2W2:
Iris Battle - An amazing tune to complement a battle that seems to prioritize atmosphere over everything else (although the battle itself is still pretty good).
XY:
Laverre City - Pretty fitting for a city that has a human-sized dollhouse and a 13-hour clock. Enough said.
ORAS:
Zinnia Encounter - I like Wally's battle theme, and it's impressive how much his character arc improved in ORAS, but I still don't think he really fits that theme as well as Zinnia does her themes.
SM:
Seafolk Village (Night) - Peaceful, calming, beautiful... no joke, I actually meditate to this music sometimes.
USUM:
Giovanni Battle - The 8-bit intro is kind of cool, but the real ace is how imposing the orchestrated remaster of his original theme sounds. If only Team RR would actually do more than just taking over Aether Paradise.
SS:
Hulbury - I dig some quality blues music, and this delivers.
SS DLC:
Mustard Battle - A fitting tune for a final battle on an island full of Japanese-style architecture with a sensei that uses a Gigantamax Urshifu.