Honorable Mention, only cuz it's an EP ... Meshuggah - I
Wow. Never thought I'd hear put one of their albums in any list that wasn't titled Fuck These Bands. :Spin: I'd have to say that is their best album though, there's a section toward maybe the 8 minute mark where my head feels like it is spinning around like Linda Blair x10.
Umm, here I'll make a list. In no particular order:
Tool - Lateralus
Kayo Dot - Choirs of the Eye
Jerry Cantrell - Degradation Trip vols. 1 & 2
Negura Bunget - OM
Electric Wizard - Dopethrone
Yakuza - Transmutations
Rwake - Voices of Omens
ISIS - Oceanic
Neurosis - A Sun That Never Sets
Meshuggah - I
Radiohead - Kid A
Ulver - Perdition City
King Crimson - The Power To Believe
Nine Inch Nails - Ghosts I - IV
Pearl Jam - Riot Act
Enslaved - Mardraum: Beyond The Within
Agalloch - The Mantle
Hammers of Misfortune - The August Engine
Orodruin - Epicurean Mass
Reverend Bizarre III - So Long Suckers
Queens of the Stone Age - Songs for the Deaf
Drudkh - Autumn Aurora
Colour Haze - s/t
A Silver Mt. Zion Memorial Orchestra and Tra-la-la Band - He Has Left Us Alone But Shafts of Light Sometimes Grace the Corner of Our Rooms
Beck - Sea Change
Technically I only really consider the Tool and Kayo Dot albums to be masterpieces. The rest are pretty close though. Honourable Mention to Deathspell Omega and Old Man Gloom, entire discography from each one.