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While not a favourite, I did have this one saved, so yeah

The recurring appearance of the DOMO office in a variety of iterations in the Xuan Yuan Sword series. Images

I thought the Santa Claus in DayZ Standalone was pretty neat.

The Uncharted references in "The Last of Us" I love me some Uncharted :)

These http://www.ign.com/wikis/the-last-of-us/Easter_Eggs also there is a paper in the beginning of Uncharted 3 makes reference to The Last of Us

Well I have many favourite Easter Eggs, but since i've played call of duty most of my life, I'd say the only easter egg I remember, would be the Thunder Gun on the Black ops 1 campaign

Probably Gnome Chompski. A pretty simple easter egg but I am a sucker for puns.

This one from Morrowind has ALWAYS been a favorite.

Peke Utchoo

In Mudan Grotto there's a skeleton called "Peke Utchoo", which sounds quite similar to the Pokémon Pikachu. Whoever put the skeleton in also included a note that reads, "If anyone shall ever find me, I hope I am able to bring them to laughter." The note was probably put in to make sure that the player realizes that the skeleton is meant to be a joke.

Taken from UESP.

The one that tasted like a chocolate but really, I don't know if it's easter egg, but when I used Clear skies shout at Skyrim when it was cloudy night. Those auroras were awesome :D

almost everything in Fallout2. the well monthy-pyhton one mostly :)

I used to be a huge Lost fan, so I really liked the Lost Island easter egg in Just Cause 2. When you fly over with your plane, it'll explode over the island. Once down on the island, you can find the survivor's camp along the beach, there is a smoke monster out in the woods,and you can find the hatch.

I really enjoy easter eggs, but I don't have favourite one.
But to be relevant, some I really liked:
Fallout 2's Bridgekeeper (from Monty Python and the Holy Grail - love this movie)
Fallout New Vegas: Indie had problems in the Kingdom of the Crystal Skull
Magicka: I've found Anakin's burnt body and got his 'arcane' lightsaber. Also, I found the Master Sword. Both worth mentioning :P

BF4 Megalodon

Hmm... Hyrdalisk in Warcraft 3

Or Cow Level in Diablo 2
Or hidden messages at Diablo 1 installation menu (if you make a SS, paste it into Paint and use a color bucket around Diablo you will see some smg)

In Portal Testchamber 5 you can use camera to block the doors and get the cubes into the next room. GlaDOS will say "You are not a good person. You know that, right ?"

Gordon Freeman laying dead in Wild Territory in STALKER: Shadow of Chernobyl

M'aiq the Liar, nuff said

SR3rd.... Easter Bunny in a net
B3

This one:
Red Faction

Mm, off the top of my head I'd have to say the 8bit Mario in Super Mario RPG. It's not a spectacular Easter Egg, but it gave me a good laugh the first time I ran into it.

Another favorite would be the "You weren't supposed to be able to get here" sign from Grand Theft Auto 3 and the "Hello again" sign in the same spot in Grand Theft Auto Liberty City Stories.

The Frostmourne in X-Men Origins: Wolverine was pretty cool. Random, but cool. :D

Not my favorite but I love all the silly references in LEGO: Lord Of The Rings.

Santa Claus in Skyrim Dragonborn DLC

(very minor spoilers ahead, I guess? O.o )

I loved this particular easter egg in Terraria.
When you talk to the Wizard, one of the possible thing he would say is: "I once heard that friendship is magic. That's ridiculous. You can't turn people into frogs with friendship!"

Also, in DLC Quest, you have to collect several things for a NPC, and one of those things is "134 Masyaf Flags". That one genuinely amused me :)

The Grunt in the last mission of Halo 3, LOVE IT! xDDD

Borderlands 2 easter egg about Dark Souls in one of the best ones I think think of right now.

I don't know how to link url, but i love The Longest Journey's easter egg with "star of death" monologues :)