Command
pm-disable (alias: dis)

Syntax
drush dis [project]

Example
drush dis overlay

The overlay module adds a great deal to the user experience for content creators. However, I find it a bit cumbersome for site administration. On client sites, I typically just disable it on my user account page, but if I'm just installing a site to test out a module, or during the initial build phase, it's actually easier just to disable it all together.

After typing "drush dis overlay" we can refresh the modules page, and see that the overlay has been disabled. If you'd like, you can scroll down and verify it is unchecked on the page.

Just like we downloaded and enabled multiple projects in a single command, we can also disable multiple projects with a single command. "drush dis admin_menu admin_menu_toolbar toolbar_admin_menu module_filter" will disable all of the modules at once.