illadelph12
aka Rakim Illa
Now this is interesting.
The catch with Apocalypse is that you can't really defeat him through physical means. You have to attack him through psionics or attack his molecular cohesion. Anything less won't really harm him, and even attacking him psionicly is a task because he has established a bit of a psionic minefield for telepaths that try to harm him. Apocalypse's versatility makes him a serious threat in this battle.
Thanos is exceedingly strong himself, and stated that he was weary of the day he'd battle Hulk (not scared, just wasn't looking forward to it). Apocalypse is STRONGER than Hulk, and unlike Hulk who needs his strength stimulated through anger to fuel it, all Apocalypse has to do is will his strength increase and draw upon ambient and extradimensional energy to fuel him, and it's done. He can go from Class 100 to class 1,000,000 in moments. His ability to control his molecules, morph, and alter his size and density allow him to become any substance from dextrous plasma to adamantium and beyond or as tall as a skyscraper, and he can grant himself any physical ability, like say the ability to absorb kinetic energy to fuel his strength ala Sebastian Shaw or absorb and redirect kinetic energy ala Bishop, which would render a majority of Thanos' attacks pointless. He can also morph all or part of himself into advanced machinery, like morphing a portion of his back into a propulsion drive and having jet wings extend from his shoulders, or forming rockets in his feet or back, granting him the ability to fly or move at great speeds.
I say it's a draw or Thanos out lasts Apocalypse. Thanos has gone toe to toe with Tyrant and is still standing, but Thanos within himself doesn't (to my knowledge, and without Thanos employing some sort of weapon/artifact to increase his powers, so just using his base powers) have the means to destroy Apocalypse using all of his powers full bore. I've never seen Thanos have control over the EM spectrum to the extent Magneto did in AoA to rip Apocalypse apart with adverse polarities at the molecular level, and though Thanos does posess psionic energy blast attacks, he doesn't have the telekinetic abilities of Nate Grey/Cable/Stryfe (two of which were BRED to defeat Apocalypse), and if Apoc employs the Shaw/Bishop ability as I stated before, though Thanos has very powerful cosmic energy attacks at his disposal, they are countered, as well as any other blast Thanos could emit because it's a form of kinetic energy.
They could fight and counter until Apoc needs a new host body in 5000 years and then Thanos would win.
Or Thanos could use a Cosmic Cube, Infinity Gem, Infinity Gauntlet, or Heart of the Universe and erase Apocalypse.