You know, I'm pretty sure Apoc is intelligent enough to come up with something Kryptonite-like or "techy-magical", if you will, to beat Superman. However, Apoc seems to be the all-time, classic underachiever. He'll FIND a way to lose. Also, DC would never have their favorite guy lose to someone (Apoc) who continually loses to people lesser than himself.
Apocalypse with out a doubt. last time a checked Magneto, Lex, Dr. Doom, Joker, Venom, Green Goblin all lose too....sure Apocalypse loses but it usually takes a lot for him to lose...him against one guy even if the guy is Superman doesn't mean Supes would win...you have to reach deeper than Apocalypse alway loses...all bad guys always lose...sooner or later. meditate
I have to admit this is a differant fight, but let's say you.. Isn't Appocalypse more or less something Supes has already handled before?
Darkseid.
Mongul.
Appocalypse may put up a good fight, but you can't beat the son of Krypton. Perhaps your biggest flaw in this battle was pitting a hero up against a villain, it's always apparent who will win..