Apple sent out an email today asking developers in its various programs to go ahead and get their applications ready with the Developer ID program, which is basically a new form of certifying apps that run on your Mac or iOS device. Developers can request a certificate through the tools included in Xcode, and then when Mountain Lion arrives and Gatekeeper is running on your Mac, developers can include that certificate and install and run their apps without issue.
You will still be able to run apps without a Developer ID included (for now), but Apple says you will get a warning when doing so. Apple's pitching Gatekeeper as a way to keep users from running malware on their Macs, but of course a program like this also helps 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, so that when Mountain Lion arrives, their apps don't face any issues. Apple's also posted a guide to getting started with Developer ID, so if you have any other questions, you can sign in with your login over there and read through it.