Gus Van Sant actually wanted Matt Damon and Ben Affleck to add a scene in Good Will Hunting where Chuckie dies in a construction accident. But after reading the changes, Van Sant agreed with Damon and Affleck that it was a terrible idea. So Chuckie got to live!
Source

Director Gus Van Sant actually painted the picture that hangs in Sean Maguire's office in the movie. So does that mean that Will's tear-down of the painting actually applies to Gus? You be the judge.
Source

You can call them sappy, but Matt Damon and Ben Affleck actually cried on the first day of filming Good Will Hunting when they saw a scene between Robin Williams and Stellan Skarsgaard.
Source