In several episodes of season four Neal talks about how his mother told him he got his father's eyes. In real life, Matt Bomer and Treat Williams are both descendants of the Baldwin family from England who have blue eyes.
In the episode where Neal, his father, and the Burke's are at dinner, El calls the duo out for feeding the Pot Roast to the dog. She then goes on to say that Peter cooked it; however in previous seasons it's said that Peter is famous for his Pot Roast and, therefore, not likely he would have burned it tonight.
In one conversation, Mozzie played by Willie Garson, talks about the many conspiracy theories people believe in. In that conversation, he mentions a stargate. Willie Garson played Martin Lloyd in Stargate SG-1 (1997). Martin Lloyd was also a conspiracy nut like Mozzie who approached the SG-1 crew about the Stargate.