Two-factor authentication is one of the most important security features you can enable. We've had it on Apple IDs for a while, but it didn't work with all Apple services and apps. Today, Apple enabled the feature for iMessage and FaceTime.
Before today, if you tried to log into iMessage or FaceTime on your Mac or iPhone, you wouldn't be prompted for a code -- even if you had two-factor authentication enabled on your account. Starting today, you'll see a bit more security in each app. iMessage and FaceTime won't ask you for a code, but you will have to use an app-specific password to log in, which you can get form your Apple ID account settings. It isn't perfect two-factor authentication, but it's more secure than just your regular password.
If you've logged into your Apple ID through your Mac or iPhone's settings, then you shouldn't notice a difference -- this only affects logging in from the app itself. Hit the link for more details.
Apple Enables Two-Step Authentication for iMessages and FaceTime [The Guardian via MacRumors]