Today I noticed the checkbox for email notification is gone for new questions. Why did it disappear?
It will be coming back, but it is dying its hair neon green first.
We are in the process of improving the email notifications. Instead of getting notifications for questions you check the box for and nothing else, email notifications will be driven by your inbox, including comments and other things that are part of the inbox.
We needed to remove the part of the UI you noticed in order to roll this out. We'll be re-adding a note and link for inbox notifications soon.
In the meantime, if you open your inbox now (where it says Stack Exchange at the upper left and red numbers appear when you have something new), at the bottom of that there is an "email settings" link that allows you to turn on the emails.
Update: inbox emails are now live.