Too many to list really. Certainly thought Lost Highway was boring until I gave it a proper listen and realised that it has some great tracks. Didn't rate HAND until I listened and realised how addictive WSYCGH is.
Sadly, prayer becomes samey if you listen to it for the thousandth time.

My biggest opinion change was probably on these days. I thought it was depressing and crap but then one faithful day I heard something to believe in an considered the lyrics. They were incredible and began my love of the album.