Real Phone Number
The phone number printed on the sign for the construction company that they are working for is the actual phone number of a Woburn, MA construction company that Matt Damon worked for while going to high school in Cambridge.
Matt Damon's Father Makes a Cameo
In the scene where Will and Skylar are eating at an out door cafe, you can see Matt Damon's father sitting in the background.
Book Reference
When Matt Damon co-wrote "Good Will Hunting", he mentions the book "A People's History Of The United States: 1492-1992" by Howard Zinn. Actually, Zinn lived on the same street in Newton, Ma. as Damon's family. The book's sales skyrocketed after the movie.