Gohan & Cooler (Dragonball) vs Percy Jackson & Luke (Percy Jackson)
Something tells me DBZ will win, but I just don't know the verse's well enough.

Drizz’t & Mina (Dungeons and Dragons) vs V & Xykon (Order of the Stick)
14-15th level wizard and 21+level Lich sorceror is powerful. However Mina is apparently a god. I think somebody who knows Mina needs to do an explanation of her. In DnD you can generally bet on gods to beat even the most powerful mortals.

Fighter & Black mage (8 bit theatre) vs Luffy & Crocodile (One Piece)
No knowledge. Pass.

Lucy & Hades (Fairy Tail) vs Saber & Berserker (Nasuverse (Fate/stay night))
No knowledge. Pass.

Beowulf & Basilisk (Fairytales and Folklore) vs 4th Hokage & Orochimaru (Naruto)
"Basilisk" is a vague term. Anything from a serpent-bird, to a moderately sized lizard, to a gigantic monster snake. Powers ranging from instant death vision to petrification to trailing poison.

Assuming the Basilisk is a giant lizard with petrifying sight, I think it would make for a pretty nice steed for Beowulf. Not as nice as Fafnir though.

Beowulf himself is an impressive character. Superhuman feats include ripping off arms and swimming underwater for three days.

I know little about Naruto though...

Sora & Sephiroth (Final Fantasy) vs Rainbow Dash & Nightmare Moon (My Little Pony: Friendship is Magic)
Shadowbolt Rainbow Dash and Nightmare Moon is a pretty cool pairing.

I predict controversy over the power levels of Sephiroth. Characters from FF7 have at various points, been taken down by swords and tanked blasts that destroy moons. Sephiroth has an awesomely crazy supernova attack that doesn't actually make sense.

In all honesty, the Square characters probably have this won unless Nightmare Moon can pull some friendship destroying tricks to turn Sora against Sephiroth. Just to make it easier for the ponies, I'll set the fight in Everfree forest, with the combatants starting separated.

Freddy Kruger & Jason Vorhees vs Sub Zero & Reptile (Mortal Kombat)
It's a fight to the victory. Not to the death. Accordingly, the powers of Jason to take punishment, and then come back from it doesn't really matter. The power for Freddy to strike in dreams doesn't matter. While the mystical superpowers and immense skill of the Mortal Kombat folk does matter.

Edward Elric & Scar (Full Metal Alchemist) vs Samus & Dark Samus (Metroid)
A fight I'd like to watch, I can imagine a lot of pyrotechnics occurring. I would definitely give it to the Metroid verse though. The Alchemists would need to close in and dematerialize the suits before they could do any real damage. That would be a very tricky feat against the mobility that both Metroid characters have, especially while avoiding their impressive firepower.