The Creek Drank the Cradle is probably the best value and the coolest album all the way through, but Endless Numbered Days is smoother and easier to listen to as well as having some of my fav. songs (Naked as We Came, Sunset Soon Forgotten). The Sea & the Rythym is a lot like TCDTC, the same for Passing Afternoon to Endless Numbered Days. Woman King is kinda jarring, but rocks out in a way that none of his precious releases does. The EP with Calexico is also really good, kinda jammy with a little bit of country/western influences and good songs. Of course this leaves out my favorite Iron & Wine song, "The Trapeze Swinger" which is only available via the In Good Company Soundrack. So, to conclude I would probably start at the beginning with TCDTC and move your way forward.
P.S. If you can catch him live, he is absolutely AMAZING, I've seen him twice and both times were AWESOME.