"Mountain Jam" from The Allman Brothers Band gets my vote. Yeah, I know it's not technically a "song" since it's not sung, but it's based on a song (Donovan's "There Is a Mountain").

Iron Butterfly's "In-a-Gadda-da-Vida" established the extended jam as a valid rock idiom, but "Mountain Jam" proved that it could be art as well. Duane Allman and Dickie Betts were great guitarists individually, but they had a symbiotic relationship that pushed their playing from the merely great into the transcendent. They fed off of each other's playing, making their joint efforts greater than the sum of the two parts that went into them. No other two guitarists have come close to musical symbiosis on the same level. And, though that symbiosis is displayed on most of their recordings, it was most pronounced in live performance and epitomized on "Mountain Jam".