#1: Tommy Tawodi - Prey
The voice actor for Tommy, a Plains Cree named Michael Greyeyes said it best when describing playing Tommy;
"Hollywood typically relegates our different indigenous cultures either into a single pan-Indian construct of some type...or, most commonly, as a historical figure, typically from a Plains culture. There are few opportunities for us to appear outside that paradigm, and when we do it is often equally narrow in focus...The writers [at 3D Realms] were always open to my comments -- which I freely offered -- and took my notes seriously, in nearly all instances changing dialogue or thematic content."
Tommy is a Cherokee Indian, and is probably the best example I can find of a well-rounded Indian character, sans war paint and headdress.
Do you have any favorite native characters that didn't make the list? Let me know in the comments below.