I would imagine it is Bohemian Rhapsody by Queen. It was so long that radio stations refused to play it, but then it could also be ANY of Meatloaf songs too.
Without giving this too much thought, two contenders must surely be "Layla" by Derek and the Dominoes and Prince's fab "I could never take the place of your man." Both have long instrumental sections but I'm certain that there will be longer chart entries that someone will remember.
The Orb produced a song in the 90s that charted and the full version of the song was about 40minutes. I do not know if this is the longest, but it must surely be a contender. Sadly I cannot remember the name of the song.
I think when Layla was issued it was as a single, and although the piano-led instrumental (the best bit) may have been on side, side one cut off before it got there.
If we're talking of "singles" in the normal (old-fashioned?!) sense of fitting on one side of seven inch vinyl, I doubt The Orb's 40-minute epic really counts! I think "Hey Jude" may actually be longer than "Bohemian Rhapsody", and another long one I think was "O Superman" by Laurie Anderson. A sneaky contender is "I Am The Beat" by one hit wonders The Look. The final groove kept repeating, so in theory the record was never ending...
Thanks to everyone who answred this question. Now Moswell and Eddy mention it, I do remember reading somewhere that it was The Orb's "Blue Room", so I think that settles this one.