I was in the Shibuya Tower store back in September, and it was rocking.  All 7 or 8 floors of it.  Massive selection.  They even had an Allan Holdsworth feature section, with cardboard display and everything.  In traditional Tower fashion, they slip in recordings of dubious origins.   The DVD floor was interesting too.  Unfortunately I cant read Japanese... and the people who work there dont speak much English. 

-Jody