My favorite Easter egg?

Skeleton in fridge in Fallout New Vegas, reference to Indiana Jones and the Kingdom of Crystal skull.

One of my favorite video game easter egg/secret moments is the classic "Ask me about Loom" from the original Secret of Monkey Island. The reason is because I actually played Loom as a child, so it was neat to see a callback to a previous LucasArts game that a lot of people still don't seem to know about.

my favorite easter egg is the evidence that the joker was hiding and torturing robin at the same time we played arkhan asylum, with the wheelchair in a cell with the wheel always turning (reminding us of that scene in arkhan knight) and in the cell with the red drawing of a puppet and mentions of the joker, of course later in arkhan city the first or maybe the second audio that the joker sends us saying that he hid something right behind our noses in arkhan asylum (many people say that he is talking about venom but for me he is talking about robin), anyway sorry for the huge text and for the possible English mistakes I'm using a translator.

I guess Borderlands 2 as the whole, the game is so stuffed with easter eggs and jokes I consider it easter egg as a whole. If I have to choose one, it would be probably the hidden Minecraft room (I don't like Minecraft at all, but this one was brilliant) :-D

Ok, I have to go with the old Fallout games as this was before Internet came into my world.

But the finding the Tardis, Godzillas Footprint, The Tin-man and MP's The Knights of the Round Table (and subsequently the Holy Handgranade).

Using No-Clip in Duke Nukem 3D to explore areas of the level you normally couldn't access and being called out on by the designer, Levelord. - - "You aren't supposed to be here".

Sifu
In the beginning of game is fight sequence in hallway with camera from side and this sequence is homage for korean movie Oldboy and similar fight in.

Finding Ash's (Evil Dead) skeleton in a cave in Mad Max. Found it as I was exploring and as soon as I saw the chainsaw I knew who it was.

My favorite Easter Egg was in Baldur's Gate 1

There's a wandering encounter with an NPC actually named "Lord Foreshadow". When you talk to him you can ask about the city of Neverwinter, and he says you should go there -- "it used to be quite popular in those nights"

Assassin body in the Witcher 2. Made me chuckle

In Wasteland 1, I think it's in Needles, there's a bookstore with stacks of Mercenaries Spies & Private Eyes rulebooks.

This is reference to the RPG ruleset that Wasteland is based on.

In SAINTS ROW there's a used bookstore named READ FICTION which references the RED FACTION series. The logo and font are also the same.

Honesty the Easter egg that sticks with me is in the Witcher 2. In the beginning when you find a dead body dressed exactly an assassin from assassin's Creed laying next to a pile of hay.

The UFO Endings of the Silent Hill series are my favorite easter egg

Imagine surviving Black mesa, Xen, killing your way through US army and alien invasion forces, then accepting deal and being frozen in time to show up in City 17, fighting your way, AGAIN, in the end exploding citadel JUST to die in an anomaly in Stalker Shadow of Chernobyl...