/admin/modules and Views Edit pages take forever to load
I found more information on this and have fixed it.

I guess that when Drupal has enabled modules that are missing from the filesystem (this happened as we're using Capistrano to deploy and I didn't sync the two sites correctly), it recursively keeps calling file_scan_directory() trying to find the missing modules, and that causes the site to timeout.

References:

Avoid re-scanning module directory when multiple modules are missing

Drupal 7 speed issue: file_scan_directory called > 1000 times per page load

Used XHProf to see what the call stack looked like over the course of loading /admin/modules and found over 5,000,000 function calls. By contrast, any other page had about 30,000 ~ 50,000 function calls.