The issue

We ran into a weird situation once, in which a user could not update anything. Trying to update Adobe Flash ended in an immediate error (Application Initialization Error), launching the Mac App Store led to the App Store saying it couldn’t be contacted, and Chrome saying it was updated when it was several versions behind. Pretty much anything that had to contact a server for updates… couldn’t.

The solution

After rebooting, checking for malware, failed proxy connections, and a bunch of other potential issues, we found out that the /System/Library/Keychains folder was empty.

So we copied the contents of that folder from another Mac, and then, magically, everything worked!

Very obscure issue and obscurer solution. Thanks to J. Pruden for finding it!