I'm not sure if these actually qualify as Easter Eggs, and it might be a little cliché... but my all-time favorite Easter Eggs both exist in The Witcher 3. The first is when Ciri describes landing in "a futuristic world where people travel around in flying machines" (aka, describing the Cyberpunk world)... and my second favorite is when Geralt looks at us (the player) and more or less says goodbye / tells us to rest (at the end of the Blood and Wine expansion).
I've been a gamer for over twenty-years now... and I mostly lost interest in video games 6-7 years ago, so The Witcher 3 was my last truly memorable experience in gaming... and yet that game somehow managed to keep me invested all the way through and provoked a visceral, emotional reaction from me that is hard to describe when compared to others.