Sure you're not thinking of starcraft? wait... thats a cheat sorry.

As far as I know, there wasn't a secret cow level in Diablo 1, but there WERE 3 cows. And because of them, a ... Diablo-legend started to spread, that there IS a cow level and no one actually knew how to get there. I think Blizzard actually included cow level in D2 because of these rumors

Anyone know what the gem on the diablo 2 battle.net chat screen did? All I know is that if you clicked it enough you got the message perfect gem activated, though to this day I still don't know what it was for.

Dopefish in Sin episodes.

if you did it right, you could fight john romero as the end boss in doom II. i forgot how though.

I'm pretty sure that D1 DID have a cow level in the Hellfire expansion, I think there was some special town portal scroll that took you there or something

idclip then just walk into the evil wall texture that somehow passed for an end boss.
As for other game secrets:
The longest door code in Deus Ex being 8675309 (I feel really bad for whoever had that phone number when that song came out)
An out of the way room in FEAR where some J-pop song played over a radio, IIRC it was a song from Shogo.
Also the Toilet fishing reference from Silent Hill 3. For those who don't know here is the original scene and here is the easter egg. And the ufo endings from those games were nice as well.

I remember coming up on this accidently and thinking...uh...wtf? While on F.E.A.R though, it's not really an easter egg, but in F.E.A.R 2 one of the characters has Shogo II posters in his room, and if I remember correctly, also a Shogo II t-shirt.

Now you mention Shogo, I remember there is a Nerv poster (from Evangelion) in main character's room.

Seeing an article in a Nintendo Magazine about getting red blood in Mortal Kombat on the SNES.
Selotape a penny to the top of the cartridge, and hit these buttons in order at the menu select screen.
I tried it for near on a month... well right up until the next publication came out saying it was a good april fools joke.
At which point I pretended I knew all along and the joke was on them.

Are you certain?... some say it was
:P

Heh thats pretty much the way you softmod an original xbox, in order to unlock the HDD, you have to pull the IDE cable from the HDD at a fairly exact moment and quickly whack in another running from a PC in the space of about 5-8 seconds

Don't tempt me :-/

Hmm, I never heard of that. I did play Hellfire and can't recall a cow level. Some sleuthing reveals the following however:
"The Hellfire expansion gives a tongue-in-cheek nod to this rumor: if cowquest is added to command.txt, the Farmer's Orchard quest is replaced by a Cow Quest. Lester the Farmer is replaced by a Complete Nut who is dressed in a cow suit and wants his Brown Suit back. The quest is accomplished when the player returns the Brown Suit, and the quest reward is a unique armor, the Bovine Plate. The player might also find a Gray Suit, though its sole purpose is to enhance the humor-oriented nature of the quest."
So there was a cow level in Diablo 1, in a way.