This is just me attempting to make (probably wrong) observations about 5Ds
Protagonist Side
Fudou Yusei - main character, signer
Blitz, Nerve, Taka, and Rally - Yusei's friends from Sattelite
Rua - male twin, may or may not be a signer (who knows)
Ruka - female twin, definitely a signer
Tempei - the twins' brown-haired friend
Himuro - the blue-haired guy from the detention center with the bull djinn deck
Yanagi - the fun old man with the treasure deck
Aoyama - the guy who helped Yusei to win his duel at the detention center
Saiga - helps Yusei out, has issues with his past that he's getting over, stuff like that
Antagonist Side
Jeager - that clown-like squeaky guy. I don't trust his intentions at all.
Ushio Tetsu - he might reform someday, but he seems too intent on chasing Yusei right now
Takasu - pirate man captain nosehair the warden of the detention center who I really don't like and who was rather nasty
Probably Just Neutral
Uryu - that guy from episode 2
Mukuro - that guy who keeps challenging Jack for one reason or another
Akutsu - moooooOOOOOmentum! He's most likely clueless.
and the various other people who have shown up as random opponents in the tournament or who have no names
Side Unknown / Unplaced
Jack Atlus - signer, used to be Yusei's friend until he ran away. It seems from here like he's being used and doesn't know it, though I'm not sure for what
Mikage - she seems loyal to Jack and only Jack, really
Rex Godwin - What are that man's true intentions, really? I mean, he works with Jeager, but he claims to be doing what he does for the good of the world. And yet I don't think Jeager has the same intentions. Maybe he's being used too, is what I think.
Aki - possibly a signer? She has a dragon at least. Who knows what her intentions are though.