Here's a weird one.
In the last 6 months (maybe under 3.8 or 3.7) my users stopped receiving emails when someone comments on their posts, despite having the Settings->Discussion->E-mail me whenever->Someone comments on a post.
The weird thing is that if an administrator comments the author gets the comment email, but for any other user they don't (I elevated a normal test user to administrator to reproduce the effect - i.e. it shows it's specifically the administrator privilege and not the specific administrator account, if that makes sense). This helpfully shows that the server is able to send the comment emails, just that there's some monkey business going on which is stopping it from happening.
Any thoughts would be appreciated.