1. Don't do anything to Twilight for a full hour, just leave it running in a separate tab or something. This gets you the "Waiting Game" medal.
2. Dexter appears in the background during the Ground Hoof ending. Simply click him when he appears to get the "Hello, Dexter Morgan" medal. He's a little quick though.
3. Just watch all of the endings to get the last medal, "No Bromo".