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
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.