my top three are probably The Power to Believe, THRAK, and Discipline (is that going to get me beaten up?!).
actually, if counting non-LP releases as well, i'd pick TPTB and its surrounding releases (Happy With What You Have to Be Happy With and Level Five, although the latter isn't quite so related). i just love that record and everything that went into/came out of it. also, a bootleg from the Tool tour and then Level Five were my intro to the band, so i guess i'm more favourable to the new stuff because of that.
for the rest, i'd throw ITCOTCK and Larks' Tongues on top of the pile with Beat and Three of a Perfect Pair, and then the rest i'm either pretty iffy about (not really into Lizard and i'm spotty for about half of Red) or dislike quite a bit (Poseidon, Islands, Starless, i find them extremely difficult to get into). The ConstruKction of Light would be great if the production and drum samples were up to par; the material is definitely strong, but i prefer the live versions on Level Five (for the title track) and Heavy ConstruKction (for everything else).