I have heaps, but one of my favs would have to be from Tool's Lateralus, just because it's a song with light at the end of the tunnel, and also he sings to the rhythm of the Fibonacci sequence (the syllables of each word make up the pattern).
Black
then
white are
all I see
in my infancy
red and yellow then came to be
reaching out to me
let's me see.
etc. But I have loads more other favourite prog lyrics from numerous bands.
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