The end of "I'll Try To Fix You" when the bomb drops about the shooting in Tucson. For those hellish minutes, nobody knew whether Rep. Gabrielle Giffords would live or die, and the characters' reactions - particularly Will slipping and calling her 'Gabby' - really brings that home.
The NSA whistleblower committing suicide. This hits Charlie particularly hard, and his breaking voice to Jim, telling him to call his parents once in awhile... Ouch.
Will apologizing to the crew when the Mock Debate was cancelled. Cue slow ballad of the main theme.
Daniel's death in "Unintended Consequences". It's telegraphed throughout the episode, but still hits hard when it happens.
Will's father dies of a heart attack while Will is on the air. Despite being estranged, Will is only almost successful in hiding his grief.
52 days after ACN had to pass the story of Equatorial Kundu off to Associated Press, essentially burying the story to a lesser release, the source commits suicide on the steps of a government building. It's essentially written off as a crazy nobody making a nonsense protest against guns. Their sacrifice may never be known to anybody except a few people at ACN.
Charlie's death from a heart attack at the end of Oh Shenandoah.