Yeah everyone has some really good ones listed.  Bowie is definitely in there for me.  Lyrics that stand on there own.  I gotta say though, having recently seen him in concert, I gotta say Lou Reed is fresh in my mind.  Very caustic, he makes his point so incredibly.  Blunt and beautiful.  This one's maybe deeper than others, but pretty killer.  I was blown away when I first heard this and read the lyrics.
Dime Store Mystery
        He was lying banged and battered, skewered and bleeding
        talking crippled on the Cross
        Was his mind reeling and heaving hallucinating
        fleeing what a loss
        The things he hadn't touched or kissed his senses
        slowly stripped away
        Not like Buddha not like Vishnu
        life wouldn't rise through him again
        I find it easy to believe
        that he might question his beliefs
        The beginning of the Last Temptation
        Dime Story Mystery
        
The duality of nature, Godly nature,
        human nature splits the soul
        Fully human, fully divine and divided
        the great immortal soul
        Split into pieces, whirling pieces, opposites
        attract
        From the front, the side, the back
        the mind itself attacks
        I know the feeling, I know it from before
        descartes through Hegel belief is never sure
        Dime Store Mystery, Last Temptation
        I was sitting drumming thinking thumping pondering
        the Mysteries of Life
        Outside the city shrieking screaming whispering
        the Mysteries of Life
        There's a funeral tomorrow
        at St. Patrick's the bells will ring for you
        Ah, what must you have been thinking
        when you realized the time had come for you
        I wish I hadn't thrown away my time
        on so much Human and so much less Divine
        The end of the Last Temptation
        The end of a Dime Store Mystery