Newbie here. (Newbie to the site/forums, but a rabid NIN fan since summer of 1991.) Hope yall don't mind if I join the party.
My vote is for
The Great Below.
My list (please forgive the commentary; can't help myself; what you all have created here is way too fun):
1. And All That Could Have Been (my favorite album; my favorite song; perhaps I can't separate myself and look at it objectively any more)
2. Ruiner (so many, many layers, dropped on top of each other, then pealed away, then back; a Nine Inch Nails archetype; even has a horn section

)
3. Last (call me childish and hyperbolic, but I don't think there will ever be a better metal/industrial song; opening is like running full speed into a wall)
4. Right Where It Belongs (somehow simultaneously an anthem and anti-anthem)
5. In This Twilight (such beauty, yet with pounding drum and Jesus and Marychain guitars)
6. Head Down (I like Discipline more, but HD rocks, and shows what he can still achieve in terms of violent sound with the most minimal production)
7. The Great Below (pure beauty; would have charted higher but not a fan of it's outro)
8. [31 Ghosts IV] (never really gave this song thought until seeing it on your list; I'm more of a 26 Ghosts III guy)
9. [Head Like A Hole] (seminal, classic, perfect, tired)
10. [Now I'm Nothing] (had missed this before; glad you guys introduced me to it; as someone else said, I'm surprised Metal didn't take this category)
Thanks.