Haha, funny, I was just thinking about this today!
MY POKEMON FICS' SOUNDTRACKS:
The Path of Destiny
Through the Fire and the Flames - Dragonforce
How Far We've Come - Matchbox Twenty
Soundtrack from Balto
Our Solemn Hour - Within Temptation (Climax Scene)
Bless the Child - Nightwish
Someone's Watching Over Me - Hilary Duff
Somewhere - Within Temptation
Crash and Burn - Savage Garden
Monster - Skillet
What Have You Done - Within Temptation
In the End - Linkin Park
Me Against the World - Simple Plan
Not Ready to Make Nice - Dixie Chicks
Hello - Evanescence
The Chosen One - ???? I don't know who sings this song! It's this song: Click!
(This was the earliest "theme song" for Cyclone. Not sure if it fits him much, but I like the mood of the song and the "chosen one" thing (referring to the Forbidden Attack).)
How to Save a Life - The Fray
Disturbia - Rihanna (For when the Forbidden Attack makes him...start to loose it)
I know there are a TON more, and I forgot them .0.
I think Thunder used to have like 20...
I'll update this if I think of more I guess. Plus there are a bunch of soundtrack songs that I can't be bothered to remember.
Redclaw, Wildflame, Spark, Nightshade, and Rosie are sad they do not have songs yet. =C
Tomorrow - SR-71 (The story's 'theme song'!)
Pokemon Mystery Dungeon 2 soundtrack
I'm Still Here (from Treasure Planet!) This is Kinje's theme song.
Colors of the Wind (from Pocahontas)
Iris - The Goo Goo Dolls
Rockstar - Prima J (Hahahaha xDDDD)
I can't list more because they hint at spoilers :c