I know Apocalypse has beed defeated several times, but I was wondering most of the stories where he is defeated are when he is trying to pull off a decades/centuries long plan together to get the perfect host body, of to prevent him from entering a revitalization chamber, or 
some other such thing. Has Apocalypse ever been defeated while at the heights of his powers?

I don't know if you'd count Magneto's victory over him at the end of the Age of Apocalypse storyline (it being AU and all). Mags took him down at the center of his empire, so I don't know how much more of an advantage Apocalypse could have had.

I'm pretty sure that the AoA anniversary mini was set 5 years after the main AoA arc and Apocalypse was still dead and Sinister was the new big bad