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'