I guess most current fans, and recent converts, dig In Absentia most. They really made a stylistic switch there. I'm a pre- In Absentia fan and for me it's very hard to pick between Lightbulb Sun, Signify or even Recordings. Stupid Dream has always been a bit too weird, and while I love the early experimental krautrock experimentation those albums weren't as strong as say Lightbulb Sun.
Up the Downstair - the original disk, not the re-master where drums and many vocals are re-recorded and all emotion found in the original disk is lost. That re-master is a travesty and it's a shame that so many will not hear the album as it should have been.
I can't listen to PT starting with In Absentia and on. They lost the magic that they had on earlier albums and everything they made afterward sounds uninspired and dull. My favorite tracks though are "Radioactive Toy" and "Nine Cats" from On the Sunday of Life. Signify and Sky Moves Sideways has some magical tracks as well, and Lightbulb Sun is my favorite out of the pop phase PT, but it still has that dreamy, almost narcotic quality that made their early sound so memorable. Recordings is a great disk too with some solid tracks.
I do miss Wilson's solos. His tone and touch on the earlier, more electronic stuff was incredible.
I have to say that if I were to have to vote for the one album I like best, it would be In Absentia. But you asked which was their best studio album, which means special effects and atmosphere and such. In that case I voted for The Sky Moves Sideways.