Alright here are the Easter Eggs I've found so far, some may or may not be Easter Eggs or not but hey.
Here's my Youtube channel, with a Video of all of these!
And the next link is directly to the video
1. At the beginning of the episode, there is a crashed helicopter in the drug store with a pilot in it. The pilot looks a lot like the pilot in Telltales Jurassic Park episodic game, who has a very untimely death.
2. When Lee is investigating for who was taking supplies, Duck is going to be Lees 'Ward' referring Lee to Batman and himself as Robin.
3. A funny one was when Duck finds the chalk lines near the motor inns gates and asks Lee for a hi-5. If Lee gives him one the update will say "Duck thinks you are totally awesome."
4. When you get on the train and find the clipboard, there is a magazine in the back with an image on it. I'm not sure what it is but it looks familiar. Anyone else know?
5. The last one I found was the best. When you go up to Kenny in the control car to tell him to stop the train, when you get to the following dialogue:
Stop. The. Train.
You're in denial!
This isn't about Duck.
Choose the ... option. Kenny will speed up the train, the same option will appear again, choose ... again. He will push you out of the car and lock the door. Lee will walk back to the box to find it covered in blood and bits of flesh.. and Clems hat on the ground. Than Duck will walk towards you as a walker. In shock Lees mouth is gaped open, Duck comes to him and Lee falls out of the Box car. The "You are dead" screen pops up.