The self-titled debut is fantastic. I don't like The Dark as much, although it obviously has great moments.
Blessing in Disguise is probably my favorite - agreed it doesn't sound great, but the material is so strong, I can get behind it anyway
Human Factor is very good, but (this might be a tad controversial, who knows?) I think Hanging in the Balance is even better.
If you haven't heard it yet, please do - it IS indeed much better than the cover suggests! It came out at such a weird time, and in some way it is a bit of weird album, period. Not really "experimental", per se - there plenty of classic sounding songs - but I'd say there some slight tangents relative to the typical Metal Church sound. The two longer tracks, Little Boy and End of the Age, are pretty phenomenal. Then Gods of Second Chance (with Jerry Cantrell guesting!), Losers in the Game, Waiting for a Savior and so on...great stuff!