Tear Jerker / Alpha Protocol

• Mike's Heroic BSoD if you fail to rescue Madison.

  Marburg: Or people you care about will start to die.

  Madison: Mike! Mike!

  (echoing gunshot)

• If Madison is killed and Mike knows that she's Alan Parker's daughter, then Mike can tell Parker that Marburg killed his only daughter. It's the only time Parker doesn't show an emotion that's either a smirk or unemotional crotchetiness - instead, his face collapses in genuine grief, before he tells Mike to go away.
• Killing Sis aboard the yacht, because on the news after her death, she gets mistaken for a prostitute and the newscasters speculate that she might have been lured aboard the yacht by a wealthy owner for the purposes of making a "snuff film".
• Mike leaving his PDA in a phone booth before he surrenders to Darcy, especially if he has a positive relationship to Mina. If he has a positive relationship with Darcy, the latter looks and sounds defeated, because he knows Mike will be executed.
• Mina's death, whether you don't rescue her or kill her yourself (You Bastard!).