When Alan and Lora go to see Kevin Flynn at his game room they find him playing his videogame 'Space Paranoids'. After he finishes playing, he turns around to talk with Alan and Lora. As they are speaking you can see the microphone coming up from the bottom of the screen. It even hits Kevin Flynn in the hand.
Just after Tron pulls Flynn up onto the solar sailor, there is a shot of the landscape below. A hidden Mickey Mouse head can be seen in a nod to the Mouse House.