Murdoc is referred to as "Suspect 218". This is most likely a nod to the original show: His character first appears in Partners (1987) which is Episode 18 of Season 2.
Murdock wearing the mask is a call back to the original series where Murdock is a master of disguise.
Murdoc quotes from and whistles the tune of "Home on the Range", the state song of Kansas. Actor David Dastmalchian, who plays Murdoc, is from Kansas.
In the art gallery, Jack and MacGuyver stand in front of a colorful painting and MacGuyver says "I think it's a Chardin", showing that while he may be a genius with science he is a little rusty on his art history. Chardin was a French 18th century painter, known for his realistic still life paintings and portraits, far from the abstract modern painting on the wall.