For me it depends on how you classify "a song".
The longest track I've run is the Disneyland Haunted Mansion ride through mix which runs 22:28. Hey it's got music in it and the sudden sound effects and spoken areas make the speed of the ride unpredictable.
The longest "traditional" song I've run is 2112 by Rush. I count it as a single song because that's how it should be listened to.

And if you don't want to count those two then I have to go with Albuqurque by Weird Al.