Well, I thought the rank the albums was a pretty good idea and then This idea came to me.
I think ranking albums is hard, as each album has a number of amazing songs on them, as some have some not so great songs.
So I thought it would be neat to break it down by album and choose your top 3 fav. songs from each album, curious to see what songs are top choice per album.

Pertty Hate Machine:
1. SIN
2. Down In It
3. Terrible Lie

Broken:
1. Happiness in Slavery
2. Last
3. Physical

The Downward Spiral:
1. Reptile
2. The Becoming
3. Ruiner

The Fragile:
1. The Wretched
2. TDTWWA
3. The Big Comedown

[With_Teeth]:
1. Sunspots
2. All The Love in The world
3. The Line Begins To Blur

Year Zero:
1. Me, i'm not
2. Zero-sum
3. Beginning Of the end

Ghosts I-IV:
1. 28 Ghosts IV
2. 34 Ghosts IV
3. 32 Ghosts IV

The Slip:
1. Demon Seed
2. Head Down
3. Lights In The Sky

Rare/Unreleased/Other:
1. The Perfect Drug
2. Supernaught
3. Big Black Bomb