John Lennon's and Yoko Ono's Imagine has often been viewed as an atheist song. From a spiritual perspective, it can be associated with Sufi wisdom.
Anthem, released in 1992 on the album The Future, is among the first songs that come to my mind when asked about a song with a spiritual core message.
What might seem like a trivial, light popular song, can be read as a conversation between a seeker and her awakening spirit-soul.
In Love Minus Zero / No Limit, Dylan abstracts from the trials and tribulations of human relationships, and points to a higher level of purity.
Love songs are well suited to relate to several levels of understanding: from erotic references to the longing for a companion, a soul mate, up to inner processes of soul and spirit that use worldly love merely as an analogy.
Different Sides was released in 2012 by then 78 year old Leonard Cohen on the album Old Ideas. I particularly like this song because it addresses an issue I find crucial on my spiritual journey.
In their 1969 song My God, Jethro Tull distinguish between artificial religion and a lively faith in God-within-man. The song can be likened to Sufi wisdom.