Just realized I never did post my favorite tracks in this thread, which surprises me since I'm a bit of a VGM nut. So here's a quick dump of some of my favorite themes from each main series game (and some spin-offs) along with some brief thoughts on them.
RBY:
Gym Leader Battle. Hard to beat the OG Gym Leader Theme when it comes to iconic battle themes in the series. That opening as well.
GSC:
Goldenrod City. My favorite city theme. Really love the cheerful and upbeat melody on this one, especially with it now backed by nostalgia today.
RS:
Slateport City and
Victory Road. It's hard just picking one theme from these games, I swear. Slateport City is another upbeat, catchy city theme that I feel often gets overlooked alongside the other great city/town themes in these games. Victory Road is pretty self-explanatory. :p
FRLG:
Champion Battle and
Sevii Islands' "Route" Theme. My two favorite remixes here. The FRLG version of the OG Champion Theme is hands down my favorite battle theme in the series (suck it, Red/Lance), and that upbeat remix of the GSC Route 42/Lake of Rage theme really drives the sense of a new adventure after the main game is done and dusted.
Emerald:
Deoxys Battle. Probably should link this with FRLG, but the whole Gen III section is getting bulky already. Anyway this event-exclusive theme is one of my favorite legendary battle themes in the series. The GBA sound-chip goes a long way with making this theme all the more intense and sci-fi'ish.
DPPt:
Mt. Coronet. Mt. Coronet in general is one of the most memorable dungeons in the series, and this theme only adds to its charm, especially as you're scaling the mountain during Galactic's endgame. The remix that plays at the Shinjo Ruins in HGSS is also great.
HGSS:
Ho-Oh Battle. One of my favorite things about the Johto region is the whole eastern atmosphere it gives off, and this theme is a good example of the region as a whole. Catchy as hell too.
B/W:
Route 10. It's a popular pick, but we can't talk Unova themes without bringing this piece up. A great piece for the final route leading up to the league, with everything that's going on with the story.
B2/W2:
Champion Battle. Another catchy champion theme that's epic in a cute way. Reaching this battle after slugging through the game on Challenge Mode really drives the intensity of the theme up as well.
X/Y:
Route 15. Another awesome route theme that seems to have drawn some inspiration from B/W's Route 10 theme. It makes the route that leads up to the Frost Cavern all the more epic.
ORAS:
Primal Kyogre/Groudon Battle and
Zinnia's Battle Theme. The Hoenn weather trio have always been some of the most intimidating set of legendary Pokemon in the series imo, and this theme really drives the point across that you're standing up to a titanic monster with the fate of the world at risk. The original GBA theme being intertwined with the remix is a nice touch as well, especially considering you're going up against their primal forms. Zinnia's battle theme is another popular one; although I despise Zinnia as a character, her theme is badass with that violin.
S/M: Seafolk Village (both
Day and
Night). It's rare for me to like both day and night themes for a city, but I honestly can't choose between these two. The day theme sounds straight out of Zelda: Wind Waker and it gets your sense of adventure pumped to explore Poni. The night theme is more serene and reflective with that sense of adventure still intact. Both themes are quite fitting for the point in the story where they play.
And let's not forget about some of the spin-offs!
Main Theme (Pokemon Conquest): Perhaps my favorite spin-off game. It's a shame it came out at the end of the DS's lifespan and didn't garner much attention.
Greevil Battle (Pokemon XD): One of my favorite final boss themes and an epic ending to a great set of spin-offs. I realllllyyy want a sequel though. maybe some day in the near future.
Miror B. Battle (Pokemon
Colosseum and
XD): I can't bring up the GC games without bring up Michael Jackson's Mexican cousin twice-removed. Two hilariously epic themes for such an iconic character. (also
this)
Primal Dialga Battle (Pokemon Mystery Dungeon Time/Darkness/Sky): Really I could list the whole soundtrack for all the PMD games here, so instead have the most iconic final boss theme (and one of my favorite final battle themes among video game soundtracks).
Courtyard Colosseum (Pokemon Battle Revolution): Say what you will about this game, but you can't deny it had an awesome soundtrack. My favorite theme in the game. It's a shame it was used on the worst colosseum in the game; if I die young, blame it on the fog in this game.