I may not like the character, but out of the list I get the idea that Sephiroth would win. The closest match-up would be with Darth Vader, but I think Sephiroth has the power to destroy a planet, and that gives him a slight advantage.
Fontaine would just be boned.
Nightmare etc. would be okay, but Sephiroth is extremely fast and can fly, which gives him an edge over slower characters.
Magneto's probably my favourite on this list, but I can think of him beating Sephiroth or Darth Vader.
Virgil can blow me.
Wesker's not written well enough to be actually good.
The Joker's a great character, but well... no meteor... That meteor gets all the points.