My personal choice would probably be Endtroducing... but does it matter anyway? It's fun to point to one single remarkable album as being the "best of something".. but it feels better to a music lover to have many (and some are still out there waiting to be discovered), I'd say.
And let me just commend you for the excellent Flaming Lips episode, especially the unanimous praise of "Powerless", but also your defense of the linking instrumentals! I'd completely forgotten the ending stretch of the album (as one is wont to do with 60+ minute albums), but now all the songs really make sense to me even if I may not possess the same level of emotional attachment to it (or even to the Lips) that you do.