Like asking which retriever organization is "the best", picking the best duck call, or the best instructional system is largely a matter of personal preference. It's also a matter of deciding what one's end goal is. Is it to compete on stage calling human judges, or is it to be more effective in the duckblind.... They're not mutually exclusive, one can definitely have both, but the approaches may vary - depending upon the goal. (If your goal includes Mainstreet calling, I'd suggest not learning on a double-reed)
Wildfowl Adventures just posted about his buddy Keith's being the best. I tend to agree that Keith (Refugeman) Allen's is possibly "the best" out there. What WA did not mention is that he has not one, but TWO World Champion trophies that he pulls out in the duckblind, to show to passing mallards when they won't respond well to calling... 8) (OK, I'm joking that he takes his trophies out in the field, but he really is a two-time world champ) Christian also didn't mention that he himself is part of the RNT Trilogy calling instructional. The RNT stuff is quite good.
I've mentioned the Carlson system on here before. Of all the instructional systems, Carlson is either loved or "hated" by callers. Carlson's is much more "technical" than the others, focusing a bit more on "physics" and non-ducky sounding excercises, to get the operator to the endpoint. (the above mentioned were not yet available when I started) I don't know if I'd still be messing with the Carlson system or not if I were starting over today. I think the Carlson system is still an excellent choice if one's goals may include trying to get qualified for the world's in Stuttgart AND one has no access to good callers live, and must go it alone with a CD/DVD player, a call, and his time.
I think a couple things need to be looked at for a new caller, or someone looking to do more with a call. What are you looking to do? Are you looking to compete and call judges, or to be more effective in the field to call ducks? How much practice do you want to put into it? Face it, some folks really want a quickie, want to spend very little time practicing.
Callingducks.com is pretty new. I'd suggest that someone looking to get more into duck calling poke around there a little. There's a good amount of stuff there including calling forums, soundfiles, etc.