*insert cheesy pun here*
there are two different instances of Epilogue, the first one is the great fire war, and the second (separate) song with similar name is the Final 13th Epilogue.
surehunter woes also occurs in the Sneaking In(?) quest in frostval 2011, the one where you collect Coal.
magiscience occurs in Silkwood Park, also an NPC critical hit
Drakonnan Rising occurs in the last part of the Akriloth battle, right before the complete quest button
warcry of the paladin occurs in Noxus Fumes, also an NPC critical hit
chasing the darkness occurs in secret of the thorn, before meeting the guardian's ghost
drakonnan's fall occurs in EotGFW, surehunter woes beginning and end, E&E beginning, interlude between songs, and as E&E end
Hidden Blades, the final earth orb quest occurs in the Hidden Blades boss battle, followed by He is Coming.
swordhaven has its own song, probably titled Swordhaven.
full darkness has 3 parts, the introduction soft one, the medium-paced battle music between the body parts, and the fast final battle song against the overnerfed SMUDD chest.
there are also a couple others, but this is all i can remember as of now.