Where on earth did the "not junk"/thumbs up icon go in Mail?
Just upgraded to Sierra, and am unhappy it's apparently gone. I use that one often. Nothing in Messages drop-down either.
New OS Sierra removed well-used icon
emailicon
Related Solutions
You can effectively turn off push notifications for a particular email account... sort of. Go to the Settings app, and hit "Mail, Contacts, Calendars". Go to "Fetch New Data", then scroll down and go to "Advanced". For the email account whose little red badges you don't want, change the setting to "Manual" instead of "Push".
This will prevent new messages from pushing a notification icon to the home screen. However, when you open the Mail app to check your other email, the app will sync the "Manual" account with the server and you'll get a badge if there are unread messages there. So, like bmike mentioned, the real way to get rid of those badges is to get closer to inbox zero.
Mail.app has a feature called rules that enables you to automate your mail tasks.
You can define rules in the Mail preferences.
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Best Answer
I'm not in front of a Mac at the moment, but is the icon you want available when you customise the toolbar?
To check:
NOTE: - The Thumbs up icon will only appear when you've got an email selected that Mail has marked as junk mail. Otherwise it will appear as a Thumbs down icon by default. In other words, what you're really looking for is a Thumbs down icon. Add this to your toolbar and you should be fine.
[EDIT]
Now that I'm in front of a Mac running macOS Sierra, I've determined that the icon you're looking for has been replaced with a new icon (see below):
Once again, this icon will change depending on the current status of the email you have highlighted. If Mail thinks it's already Junk, then the arrow points up instead so that you're removing it out of the trash. Otherwise the arrow points down by default so that clicking on it will trash it.