The fandom is divided between the albums Music Has the Right to Children and Geogaddi as their Magnum Opus.
Their pre-Twoism stuff that was leaked mysteriously, and even if it wasn't Boards(Word of God implies they're legit, however), they're pretty awesome.
Tomorrow's Harvest is starting to be considered this by some of the fandom, with its epic, expansive sound inspired by 70s and 80s film scores.
"Roygbiv", their arguable Signature Song, is so well-loved that when Warp Records announced a 20th Anniversary box set, they let the fans choose a the of the songs that would appear in one of the CDs. "Roygbiv" won second place, only suffering by a landslide defeat from Aphex Twin's "Windowlicker".