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[Klutz64]

One of my favorite tracks in my playlist:

FF Mystic Quest - Battle Medley

The music in MQ is pretty good, but what really does it for me is the fact that the game holds the most nostalgia for me of all the SNES games I've played. First RPG I ever played. Not counting the ten minutes of the NES Bard's Tale it took for me to be totally lost and confused.

BONUS! DOOM CASTLE + LAVA DOME REMIX

[Chronix112]

Katamari Damacy!
Katamari on the rocks
Katamaritaino

[Yggdrasil]

Guilty Gear XX Accent Core - Keep The Flag Flying

Guilty Gear 2: Overture - The Fate Broke Down.

Guilty Gear Arrange Tracks Plus - Meet Again

[Chronix112]

Gex
Cemetery Stage
Spin & Puke stage 1 boss
New Toonland (Stage)

[Ramza]

Soukaigi
"Quake"
by Hiroki Kikuta

https://www.youtube.com/watch?v=wrHCkD8R_84

[Yggdrasil]

^Ah Soukaigi. That game has great music.

Soukaigi - Fire Wire

Gex
Cemetery Stage
Spin & Puke stage 1 boss
New Toonland (Stage)

Really enjoyed all of them. :)

[Holykael1]

I love this sort of topic!

Ys Seven - Desert of Despair (only the best desert theme ever created) : http://www.youtube.com/watch?v=KnrObjp6RXg
PW:Ace Attorney - Objection 2001 ~ Cadenza Remix: http://www.youtube.com/watch?v=GajrbFTB_3o (Sounds so energetic!)

[Darilon]

White Knight Chronicles - The Travelers
I was not the biggest fan of the game but thought this piece of music was great.

Guardian Crusade - Opening
Loved this game. There was a lot of music I liked from it but the opening theme sticks out.

Pokemon Black/White - Route 10
It may be just me but I find it hard to think of memorable pokemon music. This changed however as soon as I entered Route 10.

Suikoden 2 - Reminiscence
Probably my favourite music from the Suikoden series.

Shadow of the Colossus - Counterattack
I am not sure if I would enjoy this as much if I had not played SotC beforehand. It just brings back memories of battling the Colossi.

[Wild Armor]

Pokemon Black/White - Route 10
It may be just me but I find it hard to think of memorable pokemon music. This changed however as soon as I entered Route 10.

That was catchy, and since you mention pokemon now...here' are some of my favorite:

Pokemon Black And White 2 - Rival Hugh Battle Music
Pokemon Black & White 2 OST Gym Leader Battle (Last Pokemon)
Pokémon Diamond & Pearl - Gym Leader Battle! Spicy
Nintendo DS Pokémon Diamond & Pearl Super Music Collection - Route 228 (Night)
Nintendo DS Pokémon Diamond & Pearl Super Music Collection - Champion Shirona
Super Smash Bros. Brawl - Team Galactic Battle! (Pokémon Diamond & Pearl) Love that organ

And some other game music:

Glory of Heracles Music - Boss Battle
Glory of Heracles Music - Battle Theme 1
Glory of Heracles Music - Battle Theme 2
Glory of Heracles Music - Battle Theme 3

Touhou 11 - Solar Sect of Mystic Wisdom ~ Nuclear Fusion (While not the original, this is plain awesome)

Corpse Party : Ending - Chapter 3 Version
Corpse Party Chapter 5's Main Building theme Survival Horror Adventure music, or a killer dance party track?

Rune Factory Frontier - The Sweetest Time Best opening in the Rune Factory series.

Sky Crawlers - Innocent Aces - BGM 23

Burning Rangers - Angels with  Burning Hearts

Xenoblade Chronicles - Those Who Bear Their Name

Arc Rise Fantasia - Unexpected Fight

NiGHTS ~Journey of Dreams~ - When The Night Falls

And a soft finish: The Legend of Zelda: Twilight Princess - Courage (One of my favorite themes from TP.

Had to link from my tumblr for a bunch of these. Enjoy!

[Yggdrasil]

Alone in the Dark (2008) - Who Am I?

Touhou 11 - Solar Sect of Mystic Wisdom ~ Nuclear Fusion (While not the original, this is plain awesome)

I like this one more.

Subterranean Animism - Solar Sect of Mystic Wisdom ~ Nuclear Fusion

[Ramza]

Glory of Heracles Music - Boss Battle
Glory of Heracles Music - Battle Theme 1
Glory of Heracles Music - Battle Theme 2
Glory of Heracles Music - Battle Theme 3

Drives me insane that there wasn't any soundtrack release for this one. I mean, the *old* Glory of Heracles games got OSTs (some of them, anyway...). Why not this one? And with a soundtrack from Hirota-san, who's in Uematsu's new band and who did about half of the Shadow Hearts series OSTs... c'mon!

Ys Seven - Desert of Despair (only the best desert theme ever created) : http://www.youtube.com/watch?v=KnrObjp6RXg

Much as I love Falcom in general and that specific song, I take your "awesome desert theme" and raise you with THE POWER OF NIER!

http://www.youtube.com/watch?v=8pJ4Q7L9rBs "Temple of Drifting Sands" (used in the desert outside the Japanese-ish town with all the crazy laws)

[Darilon]

Soma Bringer - Idea

Rune Factory Frontier - Home
Rune Factory Frontier - Kross
Rune Factory 2 - Credits OST
Because you can never have enough Rune Factory

Tales of The Abyss - Meaning of Birth

Jeanne S'Arc - Trail
I don't know how long I left my psp on the world map while I listened to this.

Z.H.P. Unlosing Ranger - The Last Battle
I actually prefer it to The Last Last Battle music.

Portal - Credit Song
Love it but do not listen unless you have beaten the game. Portal 2 credit song is also awesome.

Professor Layton and the Spectre's Call - Final Battle

[Taelus]

*steals many of these for an upcoming music podcast*

[Yggdrasil]

from "Falcom J.D.K. BAND 2 / Dark Fact's Counterattack":

Speedy's Coming / "Battle" from Dragon Slayer: The Legend of Heroes

[Chronix112]

Tekken
Tekken 1 Soundtrack - Venezia, Italy
Tekken 1: Kyoto Theme
Tekken 1 Soundtrack - Fiji, Philippines
Tekken 1: Angkor Vat Theme

Tekken 2
Tekken 2 OST - Ring a Bell ~ King's Theme (Arranged Version)
Tekken 2 OST - Emotionless Passion ~ Kazuya's Theme (Arranged Version)
Tekken 2 OST - Be in the Mirror ~ Devil's Theme

Battle Arena Toshinden
Battle Arena Toshinden - Sofia - Theme
Battle Arena Toshinden - Duke - Theme
Battle Arena Toshinden - Ellis - Theme
Battle Arena Toshinden Gaia Theme

Battle Arena Toshinden 2
Mondo's Theme
Elis' Theme
Rungo's Theme
Duke's Theme
Sho's Theme