Here's my estimation on how things should go.
Vergil < Marth. Marth's fighting style is more practical, as Sin mentioned.
Vergil > Meta Knight. Short sword v.s. Katana = bad for the guy with the short sword.
Vergil < Link. Link has a more practical fighting style, range advantage, and skill.
Vergil = Raphael. Rapheal has skill, but Vergil's weapon has a practical advantage.
MetaKnight < Vergil.
MetaKnight > Rapheal. MetaKnight is very skilled and the rapier is much less effective against an enemy inside your range. If MK closes the gap, he wins.
MetaKnight < Marth. Marth's sword, while more effective at range, is still effective in close quarters.
MetaKnight < Link. See Marth.
Marth > Vergil. More practical fighting style and sword design = win.
Marth > MK. Dangerous both at range and in close, both are skilled, Marth's weapon is better.
Marth = Raphael. Both want to stay at range and poke each other, neither seem to have a definitive skill advantage.
Marth < Link. They're weapons are similar, but I think Link's more aggressive style would take it. I also can't see Marth countering Mortal Draw or a Helm Splitter.
Raphael = Vergil.
Raphael = Marth.
Raphael < MK.
Raphael < Link. His own creators had him lose to Link in SC2. D:!
This leaves me, with my admittedly biased opinion of
Link > all. 131
Link: 5 wins.
Marth: 2 wins, 1 draw, 1 loss.
Vergil: 1 win, 1 draw, 2 losses.
MetaKnight: 1 win, 3 losses.
Raphael 2 draws, 2 losses.