Out of his main discography (i.e., the songs he released in his lifetime), I'd choose "Cry." Michael had countless options for Invincible's token environmental/cultural awareness anthem -- "What More Can I Give," "People of the World," "I Have This Dream," "Shout" -- and yet he chose to go with R. Kelly's tepid, hollow submission. I'll never understand why.
If we're including his unreleased and posthumously-issued material, I'd choose the 2010 remix of "Chicago." I commend Cory Rooney and Taryll Jackson for pushing the sonic envelope, but it's the only Michael Jackson song that I consider to be utterly unlistenable. The production doesn't match the vocals whatsoever, and it's almost unmusical to a criminal degree. There are many counterpoints to the argument that a song can only be properly completed by its original producer -- "This Is It," "Another Day," "Behind the Mask," "Much Too Soon," "Love Never Felt So Good," "Do You Know Where Your Children Are (2010 Remix)," "Stay (2010 Remix)" -- and this tops the list in my opinion.