I'll take a leaf from wmlk (post 159) and use his format, seems like a good way to group it up.
Starting Town Theme:
NEW BARK TOWN, Gold, Silver and Crystal
Although Silver wasnt my forst pokemon game, it was the one that I understood the game better and when I think of pokemon music, this pops into my head. The start of 2 journeys, into Johto, as well into new Kanto.
Opening Route Theme:
ROUTE 101, Ruby, Sapphire, and Emerald
Really set the mood for a new adventure for me. Whimsical enough to be happy, and enough to add a sense of anticipation for what will come
"Adventurous" Route Theme (Guess I have to do 2 as well, to many good ones to pick):
ROUTE 10, Black and White
http://www.youtube.com/watch?v=465uaHc-r6AReally good feel for the route. This route was one of my favorites in terms of design. Really cool look and feel to it.
ROUTE 38, Heart Gold and Soul Silver
Like the pervious one, it really had a good feel of exploration to it. One of my favorite routes, purely because this is where I saw my first legendary llama, and the same one that I caught my first.
City Theme:
Vermillion Ciry, Heart Gold and Soul Silver
It's slow build up to the familiar theme from RBY when you first step off that ship into the very familiar land of Kanto for the first time was amazing to me as a child. HGSS captured that feeling perfectly with the xylophone.
Surf Theme:
Ruby, Sapphire, Emerald
I would hope this would be the best one, seeing as most of the map is water. All hail the glorious trumpets
Bicycle Theme:
Red, Blue, and Yellow
Cant go wrong with this tune.
Battle Theme:
COLRESS, Black 2 and White 2
I believe at this point, Colress' theme is widely accepted as one of the best themes in pokemon to ever exist. As it should be.
Gym Leader Theme:
Johto Gym, Heart Gold and Soul Silver
Really got my blood pumping, it did its job exceptionally well
Enemy Team Theme (any goes, Grunt or Leader):
The Boss of Team Galactic, Diamond, Pearl and Platinum
Really good music for the battle that decides that fate of a universe. Plus it has a bass line that sounds like a good fit in a Kirby game, you cant go wrong.
Champion Battle:
Lance/Red from Heart Gold, Soul Silver
Amazing theme. Fitting of both a cheating dragon master(3 under leveled dragonites, lol) and red, the true pokemon master.
This is a good metal cover I found browsing newgrounds years ago.
Legendary Battle (I had to go with 3, couldn't narrow it down well):
Kanto Legendary Theme, X and Y
Amazing is the first word to come to mind. Excelent theme, great throwback to the original theme at 0:50 ish. Perfect tune to catch Mewtwo or the birds to. Really miss when legends werent so easy to capture. Gimme back my capture rate of 3, not this 45 crap from Sinnoh onwards.
Deoxys theme, Fire Red and Leaf Green
Really good theme, many never actually experienced it because the Wi-Fi system wasn't in place at this point. Shame, because its glorious.
Ho-oh Theme, Heart Gold and Soul Silver
shout outs to Ho-oh from HGSS as well, those drums man
Credits Theme:
Black and White
You feel like the king of the world right now. Beat the coolest rival the series has to offer, save for Silver, and beat the game. Gets you pumped to go back and actually face the champion for real, then Alder makes you bend over with that moth from hell.
Gen 2 and Gen 5 had my favorite tracks from the entire series, and lookin gback at my list remlects this.