Crystal's title theme slightly differs at the beginning from the Gold/Silver version, but soon becomes the traditional Gold/Silver title theme. It's just as good.
Adding the Pokémon Stadium Remix. Even more win than the original, which is hard to do.
They remixed it three times, that one above is for the actual Gym Leader battles. The second remix was for the Pika Cup Semifinal, and the third for the Petit Cup Battles 4-6.
Dear Lord, as awesome as the HG/SS version of this song is, the GSC version's first few seconds tells you just two things: you're going against the original gym leaders, and SHIT. JUST. GOT. REAL.
Route 1. You step outside, you get your starter and you leave your little pokey town and venture into the world full of hope and ambition. This tune nicely conveys that child-like sense of wonder and playfulness.
HG/SS has an incredible remix of the original wild Pokémon theme. Encountering wild Pidgey will never be the same again...
Route 24 and 25 just has that perfect adventure sound to it. Despite not appearing in Gold or Silver, the DS remakes have their own version, and it's something else.
In 1999 Nintendo released a (fairly obscure) album of some of the music in Red and Blue called Pokémon Hikerukana? (Can You Play Pokémon?). The mixes of the S.S. Anne, the opening, closing and cycling themes are definitely worth listening to. A user on YouTube has the linked songs and more. Listen to it. Now.
Red. If you're not picturing yourself getting your ass kicked while listening to this, well, you might want to look into that source of heat that is your pants.
The Rival Trainer music in Gold/Silver/Crystal already sounds catchy. The remixes in Pokémon Stadium 2, however, send awesomeness to a whole new level.
Also, the brand new Summoning the Legends of Johto theme and Ho-oh and Lugia's arrival themes perfectly capture the awe and wonder of summoning and encountering the two most powerful of Johto's living myths.
The Credits Theme sticks the most out of all the tracks in the game. The HG/SS remix does it great justice, though this version of it a bit better.
New Bark Town. Probably the best starter town music in the Pokémon games. As good as the HGSS version is, there's something about the original version that just can't be topped.
As you may already know, there is a key item known as the GB Sounds which changes the music to 8-bit format. While most of the tunes are taken from the original G/S/C, even some of the ones that weren't were given this treatment. For some Retraux goodness, here's the 8-bit Global Terminal, Mart and Route 47/48.
In one minute we have: Gold and Silver's intro music, New Bark Town, Goldenrod City, Burned Tower, and the Rival and Eusine's leitmotifs.
"The Medley of Pokémon" by Hapi. It's absolutely breathtaking. Can be found on Youtube in three parts: 123. There's RBY in here too, but the majority is GSC. It absolutely FLOORS you. This video has the download link for the full version.
Gold and Silver probably has the most elegant surf theme in the entire series. The remake isn't half-bad, either
Sinjoh Ruins! Otherwise known as HGSS's remix of the top of Mt. Coronet from DPPt.
Hoenn
The SNES-like audio for the GBA did wonders for the music of Pokémon, and the whole soundtrack doesn't disappoint.
Sootopolis. It may be calmed and relaxing, but this song does tell you that you're in a legendary town. In the middle of a volcano.
Route 119. Can't take your bike through the tall grass, which people also happen to be hiding in. Not to mention that it's usually raining - and don't bother with an umbrella, lest you get struck by lightning. You're earning your way through this route.
Route 111. Almost made the endless sandstorm damage in battle worth it.
Route 104 is a fantastic piece for the first beach you see in the game.
The Battle Frontier theme. Particularly the opening few notes. The whole thing just screams "triumphant."
All of the ending themes have a triumphant note to them, but Hoenn's... is a complete Tear Jerker.
The Gym Leader victory theme in every Pokémon game is super-happy, but its Generation III rendition is probably the best of all of them; it actually makes you feel like you've accomplished something. Bask in your victory!
Route 101 is yet another great first-route tune. As if that weren't enough, though, there's actually an HGSS remix of this song! (After you get the Radio Expansion card, it plays on the radio's Music Channel on Wednesdays, and can be used to draw out various Hoenn Pokémon in the wild.)
The cycling theme is so unbelievably happy and fast paced.
Crossing the sea? No you aren't. You're going to sit on this boat for the next HOUR and listen to this incredibly awesome track loop over and over and over again.
Petalburg City. This link here is 10 minutes of upbeat pleasantry.
The Mt.Pyre/Shoal Cave/New Mauville theme. A tune which provides just the right mix of ambience and adventure to suit its locations, and is criminally underestimated when people talk about the best music of the series.
Even the "Room of Glory" music is incredible...sadly, it's another Wasted Song in the Hoenn-based games, as it only plays when Steven Stone/Wallace is recording the player's League-triumphing feat in the Hall of Fame Room.
Why hasn't the Rival Theme been added here yet? For the first time that the player's rival is friendly, this theme is both upbeat and epic at the same time!
The Deoxys battle theme is pretty damn awesome. It becomes even more awesome if you consider that you're battling a Pokémon coming from outer space!
Alone, the Kyogre flood theme is good. But combine it with the creepy Groudon drought theme and it really intensifies any uneasiness with good music. Flood, Drought.
Sinnoh
The Dialga/Palkia battle theme (Super Smash Bros. Brawl remix here for maximum awesome) and the "lake trio" battle theme from Diamond and Pearl...actually, you know what? Pretty much every battle theme in the damn series.
Challenging Cynthia. Given how she's got possibly the best temperament out of all the Champions (Steven Stone in Ruby/Sapphire a close second), the sheer difficulty in fighting her (with mostly exhausted Pokémon, mind you) and the what-do-I-do-what-do-I-do-what-do-I-do-what-do-I-do?! feel of the music makes for one epic Championship battle.
"battle gene M" is a song performed by MTM, a group consisting of Junichi Masuda on keyboards, Shinji Miyazaki on bass, and Hirokazu Tanaka on drums. This song is based off of Cynthia's battle theme, as noted in a blog posting by Junichi Masuda. More information can be found in this article.
Do Diamond and Pearl have the best ending themes? Ehh, well, judge for yourself.
The encounter themes are usually sped through after three seconds or so (barring Cynthia) but if you listen to them they're often extremely good. I present the Fisherman/Sailor theme.
The Pokémon White rendition of Opelucid City and its Blackcounterpart may sound nothing alike, but both are awesome in their own way. In particular, the White version becomes even better when you stand by a girl playing a violin, giving it a very Classical or even Celtic vibe.
The one in Black is also reminiscent of music from early Sonic the Hedgehog games.
N's Castle Bridge. Very reminiscent of Pokémon Mystery Dungeon's music.
How about N's Castle itself? It's somewhat reminiscent of Castlevania music.
Legendary Battle Theme. The song is such a mess that as soon as a melody is found it throws you a curveball. This really puts into perspective just how powerful the Legendaries really are.
On the subject of Mother 3, we have Route 10. You half expect to bump into Boney.
The Pokemon League theme when you're in the Pokemon Center or waiting to challenge one of the E4 members. Doesn't have that much, but that's what makes it cooler.
The Elite Four Battle Theme. As one YouTube commenter said: "The bass and drums [in] this song is enough to make your Pokémon faint." Well, maybe not everyone's, but still.
The Village Bridge. Starts out simple when you enter the area, but adds layers to the song when you talk to certain people scattered throughout the area.
BEST! MUSIC! EVAR!
The background theme for the EntraLink. Sounds more like an epic background theme from Final Fantasy than one would necessarily expect.
Although the Gym Battle music arguably qualifies. It starts out fast-paced and epic from the very beginning. Many consider the music that plays when you reach the Gym Leader's last Pokémon (listed under "Pokémon title theme" at the top of the page) to be even better, but others have complained that it kills the mood because of the completely different beat and pace.
Black City, and its counterpart, White Forest. The former is a haunting techno melody that seems to emphasize just how much the city is corrupted (heck, a few openly admit to being greedy), while the latter is a happy, upbeat tune with a cheerful innocence to it—perfect for a nature-filled forest. Certainly a harsh contrast, much like the opposing themes for Opelucid City.
Spinoffs
Pokémon Stadium
This folder is still in the process of being built. If you see a theme exclusive to Stadium (JP), Stadium, Stadium 2, or Battle Revolution in the other folders, please move it here.
This part of Colosseum Master Sashay's theme sounds extremely similar to part of the Cipher admin battle theme from Pokémon Colosseum. Justified, as the developer studio Genius Sonority worked on both games.
Dialga's Fight to the Finish!, the final boss of both the main story and the fifth special episode. In the latter, it actually begins to play well before the battle actually begins, serving to make the prior scene even more epic.
Ladies and gentleman, I give you the Cargo Ship/Oil Field Hideout. Note how it's a medley of several Dim Sun themes. Also, the video's picture is a spoiler, so view at your own risk.
The GameCube Pokémon games have Miror B.'s battle music. The original gave him a wacky salsa beat for his Ludicolo-heavy team, and the second game outfitted him with a funky-fresh, disco-riffic battle theme, perfect for groovin' to.
You probably used the Master Ball instantly on Shadow Lugia... but if you did, you missed out on his awesome battle theme.
The Phenac City takeover music, officially named "Cipher Command". At first you just think, "Hmm, the music is a little different." It's certainly not worse than the original, but something about it just doesn't feel right... and then the theme suddenly gets progressively more sinister until it comes to a positively demonic crescendo... and then it loops back and goes back to the pretty, serene theme that it was at first. This theme plays when, unknown to the player, Team Cipher has taken over the city with its members disguised as the various characters who are normally in the city. While this music is playing, you begin to notice things like the fact the guy running around the water fountain with his Castform suddenly has a Duskull.
And those are just the battle themes. There's also the relaxing Realgam Tower, the peaceful Agate Village, and the beautiful Relic Forest. And though it may not fit the trend, there's The Under, which is a town theme that sounds nothing short of awesome.
While we're talking about the TCG video game soundtrack, Ronald's theme because it's awesome and it reminds me of beating the absolute tar out of that jackass.
To put it another way: Ronald is Blue/Gary'sexpy. But unlike Blue, you will want to face him, if only for this awesome theme. That can't be said for most Rival battles.
The regular battle theme. Who says awesome tunes can't be laid back, especially with that bass.
The theme for Mason's Lab/the World Map is oddly soothing. Has a bit of a "getting ready to depart on a grand journey and explore the world" feel to it.
Hey You, Pikachu!'s credits. This song, in which Pikachu himself sings, may not be "awesome" in the "I just captured Mewtwo with a Great Ball" sense, but it is the cutest song that was ever sung.
Another from Hey You, Pikachu!. This game had a surprisingly good soundtrack for how simple it was.
was composed by Junichi Masuda of GAME FREAK (who is a part of the music group MTM and helps compose music for a lot of the handheld Pokémon games) at the request of Shokotan (Shoko Nakagawa) of the television show Pokémon Sunday. It was apparently played in a live performance by MTM on September 4th, 2011. As of now, it does not seem to be a "Generation 6" Pokémon game music track; it was likely just composed in the style of such game music. Nevertheless, it sounds awesome, perhaps fitting for a wild Pokémon or Trainer battle theme.
The fan game Pokemon Garnet from Pokecommunity.com has its own fair share of nice music as well composed by Tobinus, most of which are currently tentative:
The game's wonderful title theme (Version 1) sounds like a somber take on the classic Pokémon main theme, while still providing unique elements of its own that preserve a sense of optimism, perseverance, and mystery.
