There was a time games didn't take them selves 100% percent serious and allowed small secrets or easter eggs. They could range from cool pop cultural references to just plain ridiculous. And its time they were shared!
Heres my best video game secret for Monkey Island 3:
When you go down to the Blood Island beach, use "use" on the water, with some patience he will eventually go into the water. He will be teleported back to M1 where he was thrown into the water. unfortunately M1 Guybrush has drowned, if he just had been better at holding his breath.

dopefish!

Jazz 2, he is no more!

If you typed iddqd into Doom 3's console it would say "Your memory serves you well"
This is always entertained me.

Cow level in diablo 1... :)

FFFFFFFFFFFFFFFFFFFFFFFFFFUUUUUUUUUUUUUUUUUUUUUU

Dopefish in Daikatana.

All the Sam & Max references in almost every Lucas Arts adventures.

Easter eggs and references have always been one of my favorite aspects of any game. Fallout 1 and 2 are full of them; Skynet, V'ger, MTG, red suited security men, whale dropped from sky and the holy hand grenade to name few. However my favorite is golden pantaloons from Baldur's Gate, mainly for the fact that it required full series to solve, puzzled the hell out of players before BG2:ToB. :P
Cow level is a fun easter egg, one of the weird ones too. A rumor that became a reality.

My favorite easteregg has to be http://www.youtube.com/watch?v=ulqzh-MqB5Q
"That's one doomed space marine.."

Hmm... have you tried out Sacred Gold yet? There's a ton of easter eggs and references. You can play that one 2 months long and still haven't seen them all. Just two Link 1 and [url=http://sacredwiki.org/index.php5/Sacred_2:Silly_Messages]Link 2[/url] examples in case you didn't know.

Wow! They really went all out with this, that is great!
I have always loved this one. Its just a great tribute to... yes guess what game <_<

Ever played "The World Ends with You?"
After you beat the game, a secret level opens up. It's hilarious in ways that I can't even readily describe.

I thought that was Diablo 2? Did I miss it?

There was no cow level in Diablo 1.