I like the Terminator2 reference in The Dig, maybe not an easter egg per se, but still funny stuff.
When Boston asks Maggie about Brink (by clicking his picture in the dialog interface) the sequence plays in the following order:
Boston: Have you seen this boy?
Maggie: What?
Boston: Nothing!
For all of you in the dark... Boston Low was voiced by Robert Patrick, the guy who played T-1000 in Terminator 2, where he delivers this, now cult, line to John Connor's best friend.
Also if you examine your Palm PC, he replies It's T-1000 model