As much as I know that any song off this album is going to be painful...I find it particularly painful that Leper Messiah appears to be leaving first.
I remember when I first heard this album that Leper Messiah immediately leaped out at me as being a classic. You have to remember that there was not a ton of progressive elements in metal at this time. I was born in late '69, and started getting into metal around 82-84. The "metal" of the time was Ozzy, Dio, Judas Priest, Motley Crue (pre-Theater) and the like. There were some cool albums, but not alot of weird time signatures (with the exception of the occasional Iron Maiden tune...they were the most prog of any major metal band around). The "big 4" were still *extremely* underground at this point.
Metallica was in many ways, my introduction to new and interesting time signatures in metal (my Rush influence not withstanding).
When MoP came out when I was 16, one of the things that hit me the hardest were things like the 5/4 intro to Leper Messiah. It just seemed so fresh and exciting at that time. It's sortof like when you guys hear BTBAM do something really new and sick for the first time. It may seem "meh" 25 years from now....but in 1986, that approach was just mind blowing.