Long time no post. Been really caught up: Tons of work, travel, Acads. Anyway, I happened to be upgrading some old Drupal sites from 5.x -> 6.x. Here's a little SQL snippet to disable all non-core modules first.

UPDATE `system` SET `status` = 0
WHERE `name` != 'system' AND `name` !='block' AND `name` !='node' AND `name` !='user' AND `name` !='watchdog' AND `name` !='filter' AND `name` !='upload' AND `name` !='tracker' AND `name`
!='throttle' AND `name` !='taxonomy' AND `name` !='statistics' AND `name` !='search' AND `name`
!='profile' AND `name` !='poll' AND `name` !='ping' AND `name` !='path' AND `name`
!='menu' AND `name` !='locale' AND `name`!='legacy' AND `name` !='help' AND `name`
!='forum' AND `name` !='drupal' AND `name` !='contact' AND `name` !='comment' AND `name`
!='color' AND `name` !='book' AND `name` !='blogapi' AND `name` !='blog' AND `name`
!='aggregator'
AND `type` = 'module'
AND `status` =1

BTW, To all who haven't been following - Drupal 7 is in the pipeline (Been looking, reading, groping and trying the unstable releases and the CVS code (wish I had time to help) for a bit), and it looks it'll be quite something when it does come out. Kudos to Webchick and the others. Great work.