Hmmmmm that's a tough one. I can't really pinpoint my favourite, so I'll just give honourable mentions.
In the original "The time machine" If you look closely at the dashboard of the thing it says "Manufactured by H.G Wells" the guy who wrote the book (I know it's not in a game but I thought it was worth mentioning).
In Left 4 Dead, there is a Lambda shaved into Francis' hair.
In Bioshock, there is a room with a cake, it is missing a slice, and protruding from that missing slice are big round bits of the chocolate cake.
In Fallout 3, in the German town police station there were some pretty messed up calls to 911...
And the moon is winking at my banana slippers, not to mention things like the Bethesda building, Harolds big cameo and the NUMEROUS references to guys like "The Vault dweller".
On one of the downloadable multiplayer maps in Halo 2, there were two vending machines, one was red, one was blue. One had a picture of a rooster on it, the other had a picture of teeth on it.
In GTA 4, on one of the TV shows (That I'm rich one I do believe) it shows some shots of Bullworth academy, the setting for my favourite sandbox game of all time.
In Destroy all Humans two, in Russia, if you read peoples minds sometimes they say "I heard they were renaming this place city 17".
In half-life Blue shift, in a dead end with some ammo and such, there is a damaged BOX with all its contents spilled out onto the floor, those being GEARS.
And that's about all the ones I can think of right now...Oh yeah, also in left 4 Dead, Louis says "Oh man this is just like counter-strike", and in CRash course, there's a bit where steam is gushing from a busted pipe in the wall, the survivors all remark about how great STEAM is, not sure what they mean by that, that stuff burns.
