Also see the Randolph Scott movies I recommended the other day.
I don't know what you know already. The more I see the less feels obscure to me. Stuff from major directors that I wouldn't consider obscure but that not everyone puts on their "must see lists" include:
Directed by Anthony Mann (who also did Man of the West) are five very good to great Jimmy Stewart movies, the best of which are Winchester '73 and The Naked Spur. The other three are Bend of the River, The Far Country, and The Man From Laramie.
Have you seen much Raoul Walsh? He's a great director who made many good westerns amongst his other films, including The Died With Their Boots On, Pursued, and Colorado Territory.
Jacques Tourneur made Canyon Passage and Wichita, which are both terrific.
William Wellman's Track of the Cat is one of the more unusual westerns of the era.
Andre De Toth's best western, Day of the Outlaw, seems like something that might end up as a Criterion dark horse at some point.
How many of those have you seen?