Okay, in a list:
1. PRE-MORTAL COUNCIL
Spoiler
Ruin and Preservation are energies that spiritually become self-aware in the story, much as the LDS church teaches that our own spirits coalesced out of some extremely rarified matter or something. Ruin and Preservation, before human time, devise a plan for the future of the world. Preservation ends up with a secret "plan of salvation" that comes to fruition in...
Spoiler
Vin, Elend, and Sazed are all clearly described as exalted to divine stature. Sazed in particular is guided by...
Spoiler
The LDS church is fairly emphatic about a quasi-pluralist approach to religious truth. When Sazed, the rejected-by-his-own-people savior (Christ, anyone?), uses his knowledge of the world's lost religions, he almost directly quotes the standard slogan of LDS interfaith tolerance at one point. --Anyone else who read this also notice the similarity between how Sazed repaired his world and how Linden Avery defeated the Sunbane?