Too difficult for me to pick favorites, honestly. I like to let them all blur together, especially since he sang about the same themes over and over again. The albums are different flavors of basically the same thing, though I mean that in a good way. Sometimes I'm in the mood for the bigger band feel of Magnolia Electric Co stuff, sometimes the stripped down feel of his solo stuff, and sometimes the inbetween of the Songs:Ohia stuff.
If I had to name an album I'd say there is something particularly transporting about Didn't It Rain. The album "Magnolia Electric Co" is a home run, no ifs/ands/buts about it.
There's a book about Molina that came out a few months ago. It's a gripping read and very illuminating for Molina fans, though devastating. It's called Riding with the Ghost.