The talk about David Lynch's relationship with his fans and the Black Lodge encyclopedia entries, coupled with a reading of the Deer Meadow sequence of the FWWM script, have given me a new idea: Sam Stanley is David Lynch's "service" to the fans of the show, a summation of what he sees as their collective, dominant traits placed into a character that gets to go along for the ride.
Stanley is presented as intelligent yet benign, mostly standing by while Chet Desmond does all the legwork and offering occasional statements. He's in constant awe of the seasoned Desmond, alternating between the personality of partner and little kid who just got to meet Mickey Mantel. Unlike Desmond, Cooper, Albert, and Cole, who all consistently appear well groomed and maintained, Desmond is just this side of disheveled, and dresses like someone's idea of an FBI agent-- an immitation.
I believe that, quite possibly, Stanley is meant to be the fans of the series, a simultaneous glimpse into what David Lynch thinks of them, and a "Thank you" to them by letting them vicariously get in on the action. Desmond then is Lynch, or at least, the world of TP itself-- a strict father figure to Stanley who keeps him out of the really big secrets but decides to concede some random bits of knowledge, and who ultimately demonstrates respect and gratitude to him. What really made me think of this is Desmond's line in the FWWM script, "You have a good eye for detail." It seems like a compliment from Lynch to all of the show's fans, letting them know how impressed he is with all of their observations and analysis.