Dogma
The two haven't appeared in any movie together. Well, not yet, anyway.
Dazed and Confused (1993 )
Yes, Ben Affleck did star in Phantoms.
Kristen Stewart has co-starred with Ben Affleck many times. It is difficult to say, however, if any of the background actors have been in more of his films than she has.
Matt Damon stars in many movies, including Ocean's 11, 12, and 13; all of the Bourne movies, Bourne Identity, Supremacy, and Ultimatum; Good Will Hunting; Invictus. There are many more, but these are the ones I know off of the top of my head.
Dogma
The three starred together in The Good Shepherd (2006).
Bounce
Ben Affleck
The Perfect Storm - star George Clooney, Donnie Whalberg and Diane Lane in the year 2000. EDIT: The perfect Storm starred MARK Wahlberg, not Donnie. Donnie's been in the Sixth Sense, and also has a new movie coming out with DeNiro and Pacino this fall called Righteous Kill.
Mortal Thoughts
Domino