Apple - Can I reset Notification Centre badge counter for Messages?

The correct answer to this issue isn't to message all your contacts.

First close the Messages app.

Then simply open up Activity Monitor and quit the Dock process to restart it.

Here's how it looks:

Your badge count should be reset after that.

PS: You can access Activity Monitor from Spotlight (⌘ Space) by simply typing its name and pressing Enter.

Edit: update thanks to @JjP and @Toland H

Before you kill Dock you need to close Messages to make it work. I had this issue on Mountain Lion (Mac OS X 10.8.2). When Messages was open and I killed Dock it didn't help. But when I closed Messages and then killed Dock, the badge was gone and after opening Messages the unread messages appeared so I could read them.

Try to restart the dock. In the Terminal located at /Applications/Utilities/Terminal.app type:

killall -KILL Dock