馃槅
The "X-Men beat Apocalypse, and Superman is more powerful, so Superman beats Apocalypse" equation is severely flawed, especially in this versus forum.
1) The X-Men defeat Apocalypse through psionics. His powers allow him to withstand physical damage. Superman (Kal El) is not psionic.
2) Magneto defeated him with adverse magnetic fields that pulled him apart at a molecular level. The psuedo-energy powered Superman would have a chance using this method of attack.
3) In the versus forum, unless stated by the thread originator, characters are to be considered to use their powers to the fullness of their capability to win.
All that taken into consideration, Apoc would murder Kal El, save possibly the Superman with the Electromagnetic powers. He can counter everything the other versions of Supes could throw at him because Supes relies on brute force and physical attacks. Apoc can shapeshift, grant himself any physical power/ability, and increase or decrease his density. He's basically an evil Martian Manhunter minus the telepathy, but plus the ability to morph into inorganic constructs like morphing his arm into a plasma cannon or rail gun, morphing his legs or back into a warp prepulsion drive, or altering his molecular structure into the hardest substance imaginable (density control).
Like I said above, he could simply alter himself to have a Sebastian Shaw type power in which every attack Supes hits Apocalypse with makes Apoc stronger, or he could just grab Supes and engulf him in his hand, then change his hand into a ryptonite/adamantium/vibranium hybrid alloy.
He'd kill Supes.