Dr. Magnusson mentions that he will forgive Freeman about the debacle at Black Mesa involving a certain microwave casserole. This is a reference to Half-Life (1998), in the chapter "Anomalous Materials". While exploring the Black Mesa facility, you can enter a small kitchen area, containing two scientists and a microwave cooking a small box of food. If you choose to, you can keep turning the microwave's power setting up until the food inside overheats and explodes. A nearby scientist then says "My God, what are you doing?!"
The line "Prepare for unforeseen consequences" and the effect it has on Eli Vance are a reference to Half-Life (1998). The first chapter after the resonance cascade which brought aliens to Earth was entitled "Unforeseen Consequences".
Was originally meant to be shipped with "Half-Life 2: The Black Box" which would have contained Episode Two, Portal and Team Fortress 2, but it was canceled. Episode Two was released in "The Orange box" which also includes the original Half Life 2, Episode One, Team Fortress 2 and Portal.
During development, the Magnusson device was given a pumpkin appearance as placeholder art until a final version of the actual device was made. A pumpkin was chosen because it was the exact size and shape the developers wanted. While the final version of the game does not feature a pumpkin as a Magnusson device, pumpkins can be found in the house one of the Advisors is sleeping in.