Best Apocalypse story arc is pretty much everything from the first appearance of the Alliance of Evil through Fall of the Mutants. So X-Factor #2-26, Captain America #339, Daredevil #252, and Power Pack #35.
The best Sinister story arc is the one where he has the most influence but appears least. Everything from The Mutant Massacre through the X-Men battling the Marauders in San Francisco in Uncanny X-Men #222
__________________ Land of the free, home of the brave...
Do you think we will ever be saved?
In this land of dreams find myself sober...
Wonder when will it'll all be over...
Living in a void when the void grows colder...
Wonder when it'll all be over?
Will you be laughing when it's over?
Granted, during all the issues I listed, Sinister himself only appears for 2-3 pages and chokes out Sabretooth.
__________________ Land of the free, home of the brave...
Do you think we will ever be saved?
In this land of dreams find myself sober...
Wonder when will it'll all be over...
Living in a void when the void grows colder...
Wonder when it'll all be over?
Will you be laughing when it's over?
The early Apocalypse is different too. Much more of a smiling, condescending smartass
__________________ Land of the free, home of the brave...
Do you think we will ever be saved?
In this land of dreams find myself sober...
Wonder when will it'll all be over...
Living in a void when the void grows colder...
Wonder when it'll all be over?
Will you be laughing when it's over?
Yep. For me, that will always be my favourite interpretation of the character. Apart from the TAS one, though he drew heavily from that early X-Factor one anyway.
Wolverine Jungle Adventure was pretty good. Nice way to reveal apocalypse as being alive but extremely weakened from the almost as good Wrath of Apocalypse story. That one has Cyclops' most powerful on panel optic blast.
__________________ Land of the free, home of the brave...
Do you think we will ever be saved?
In this land of dreams find myself sober...
Wonder when will it'll all be over...
Living in a void when the void grows colder...
Wonder when it'll all be over?
Will you be laughing when it's over?
Wrath of Apocalypse, also known as Endgame is an X-Factor storyline where Apocalypse take up residence on the moon and puts together his Riders of the Storm/Dark Riders from Inhumans misfits. His plan is to take out X-Factor's ship, force them into a confrontation, and for lack of a better description, "eat" Nathan Christopher. Instead he just infect him with the T/O virus and he has to be sent to the future and became Cable etc. etc. Toward the end, Cyclops is supercharged by Jean and Nathan and unleashed a white/yellow Optic blast that literally vaporizes a 50 ft. Apocalypse. More or less nothing left of him. This is why he's so weak during Wolverine: Jungle Adventure and X-Cutioner's Song that he has to rely on other people to do his work for him.
__________________ Land of the free, home of the brave...
Do you think we will ever be saved?
In this land of dreams find myself sober...
Wonder when will it'll all be over...
Living in a void when the void grows colder...
Wonder when it'll all be over?
Will you be laughing when it's over?