To me an "Easter egg" is any design element that has a specific story behind it that goes beyond just "getting the job done" AND it's something most people don't know about.
I.e. -- the headlights didn't need to have a design that looks like "100" (or "001") but they do to celebrate Ford's centennial. And most people don't know about it.
Another i.e. -- the interior door pull (where you grab to close the doors) is the exact same material used for the engine brace. Check it out if you haven't. The same shape and pattern of aluminum that braces the top of the engine was used (in a shorter, cut piece) as the door pull. Ford could have just used a basic metal bar that fit well in the human hand, but they used that specific piece from the engine cradle. To me that's cool, and an "Easter egg" because most people have no idea.
Another i.e. -- the underbelly tray says "Ford GT" on it. Most of the tray has tiny bends to strengthen it, but the is a pattern where the tray is smooth that spells "Ford GT." If you haven't been under the car you'd never know it, and it certainly wasn't necessary. But Ford did it anyway. That's cool. Side note -- the first three Ford GTs, built as "2004" models (the white one is Bill Ford's) DO NOT have "Ford GT" in the underbelly pan. They hadn't thought of it yet.
I think a lot of people have noticed the exterior mirrors aren't in the same location between the driver's and passenger side, and there's a purpose to that (the thick A-pillars required them to be staggered), so that's a borderline Easter egg IMHO.
Also, the pronounced exterior lines on the doors that lead to the cooling vent/scoop were done to maintain the concept car's look while allowing the windows to go up and down. If you look at the yellow concept car the door shape actually cuts IN to make an air path to the cooling scoop. But that design makes it impossible for the window to lower. So they kept the door flat in the production cars and made the door lines flare OUT to maintain the look while allowing the windows to go down. A very effective optical illusion if you ask me, because most people never noticed...
These are the main "Easter eggs" I know about, but there are more I know I'm forgetting.