Oooh... many
Bilbo, BoTB as RB decks. I'll give it a try. Although, there are only 4 companions which fulfill the requirements, if I remember correctly: Bilbo, Gandalf, Gloin and Elrond. Only other is Smeagol and technically, there was only Gollum in The Hobbit.
As for the shadow side: Gollum, Goblins (although not Moria) and Wargs appear in the book and Sauron is mentioned.
If the chosen format is standard instead of movie, there would've been more characters available such as King Dain and sons of appearing characters such as
Brand, son of Bard and
Grimbeorn, son of Beorn.