Apple has sent email to developers in its various programs to go ahead and get their applications ready with the Developer ID program. This program is basically a new form of certifying apps that run on Mac or any iOS device.
Developers can request a certificate through the tools included in Xcode. When Mountain Lion arrives and Gatekeeper is running on your Mac, developers would be able to include that certificate and install and run their apps without issue.
For now, you will be able to run apps without a Developer ID included. However, Apple has said that you will get a warning when doing so. Apple is pitching Gatekeeper as a way to keep users from running malware on their Macs. A program like this will also help keep the app ecosystem more closed, allowing Apple just a little more control over what runs on your Mac.
Most developers, however, will probably want to go ahead and sign up for this. This is because when Mountain Lion arrives, their apps would not face any issues. Apple has also posted a guide to getting started with Developer ID. It would be easy to clear doubts now. Any question in your mind, you can sign in with your login over there and read through it.