Here is an archive of all the past top five lists I've one over the years.
The X-Men villain Apocalypse was introduced in 1986. However, his backstory soon established that he was actually an ancient mutant who had simply been operating behind the scenes for years. Therefore, over the years a number of writers have chosen to retcon Apocalypse into the backstory of various characters, revealing that Apocalypse was the one who gave them their powers. Here are the top five such characters...
HONORABLE MENTION
Wolverine
This one doesn't really count, since it never actually made its way into official continuity, but originally, in the famous Weapon X storyline, where we see where Wolverine got his adamantium skeleton, writer/artist Barry Windsor-Smith intended for Apocalypse to be behind the Weapon X project. He's who is on the phone in this scene...
You can read more about it in this Comic Book Legends Revealed, but suffice it to say that it never actually was made an official part of Marvel history.
5. Moses Magnum
After appearing in Giant-Size Spider-Man #4 in 1974 as a villain for Spider-Man and the Punisher (and seemingly killed), Moses Magnum was picked up by writer Chris Claremont as a foe for Power Man in the Power Man Annual in 1976. Drawn by Lee Elias and Dave Hunt, the annual is an interesting affair, as Luke Cage is hired to bring Moses Magnum down and rescue a scientist he had kidnapped. Magnum, at the time, was just a guy with weapons. At the end of the issue, he seemingly dies...
Two years later, Chris Claremont brought him back in Uncanny X-Men #118 (drawn by John Byrne and Terry Austin) and now he had superpowers...
A decade later, when the storyline was reprinted in Classic X-Men #25, Claremont explained where the new powers had come from in a new interlude interjected into the story as a flashback, drawn by Kieron Dwyer and Terry Austin. They had come from Apocalypse!
4. Stryfe
Interestingly enough, Cable's nemesis Stryfe, head of the Mutant Liberation Front, actually debuted one issue BEFORE Cable, at the end of New Mutants #86 (by Louise Simonson, Rob Liefeld and Bob Wiacek)...
before appearing in his full over-the-top glory the next issue...
In the final issue of New Mutants, Liefeld and Fabian Nicieza revealed what Stryfe looked like under that mask and, well, it was Cable!
A few years later, in The Adventures of Cyclops and Phoenix #2 (by Scott Lobdell, Gene Ha and Al Vey), we learn that Stryfe, a clone of Cable (we knew that already from some X-Men crossover), was given his mutant powers early by Apocalypse in the future, as Apoclaypse believed that the boy WAS the actual Nathan Summers (Cable's real name)...
Go to the next page for the top three!
3. Exodus
Introduced in the first part of Fatal Attraction in X-Factor #92 (by Scott Lobdell, J.M. DeMatteis, Joe Quesada and Al Milgrom)...
Exodus was named and established as quite a powerful being in the next part in Uncanny X-Men #304 (by Lobdell, John Romita Jr. and Dan Green)...
A few years later, in the one-shot Black Knight: Exodus (by Ben Raab, Jimmy Cheung and Andy Lanning), Black Knight and Sersi find themselves trapped in the past, with Dane in the body of one of his ancestor Black Knights. This Black Knight is friends with a crusader named Paris Bennnet, who is obsessed with seeking out power. He and Black Knight end up losing their friendship as Black Knight won't go along with him on his dangerous quest.
Once alone, he is encountered by a mysterious being, who gives him his powers...
Which is revealed later in the issue as Apocalypse...
With him being set upon his old friend by Apocalypse...
This was all based on a bit in the Bloodties crossover a few years earlier that suggested a connection between Black Knight and Exodus.
2. Living Monolith/Living Pharaoh
Introduced in X-Men #54 (by Arnold Drake, Don Heck and Vince Colletta)...
The Living Pharaoh was given an origin in Marvel Graphic Novel #17 (by David Michelinie, Marc Silvestri and Geof Isherwood)...
Years later, he is brought into the X-Men crossover The Twelve, where we learn that he was manipulated and powered by Apocalypse all along. Here he learns this in Uncanny X-Men #376...
1. Mister Sinister
We first meet Mister Sinister in Uncanny X-Men #221 (by Chris Claremont, Marc Silvestri and Dan Green)...
But obviously that was back when Claremont had a whole other set of plans in store for the villain (as detailed in this very old Comic Book Legends Revealed). Claremont left and later writers had other ideas.
In 1996, in the sequel to the Adventures of Cyclops and Phoenix, dubbed appropriately enough The Further Adventures of Cyclops and Phoenix, Scott and Jean end up in the past, where a man named Nathaniel Essex and his wife Rebecca meet En Sabah Nur...
En Sabah Nur makes Nathaniel an offer to mutate him, but he initially refuses, but ultimately it is the loss of his wife (and her hatred of him at the end) that drives him to accept...
So in the last two issues of the series, he accepts and Sinister is born!
That's the top five!