In the 4th episode, "Abe Lincoln Must Die!", there is a reference to Steve Purcell, the creator of Sam & Max. Inside the yellow mailbox is a newspaper that reads "Purcell attacked by Two-Headed Monkey!"
On the bulletin board in Sam & Max's office, there's a poster that shows a man with a water faucet for a head, stating it's a "Human Enigma." This is a reference to Sam & Max Hit the Road, where the Human Enigma was one of the freaks on display in the Carnival tent.
In the episode "Abe Lincoln Must Die!", you can change the date on the calendar in the presidential office to Easter Sunday. By doing so and going to the golf hole in the front yard, you can find an Easter egg in the hole, which does nothing.