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Tear Jerker: Radiant Silvergun
Stage Five of Radiant Silvergun is an especially tearjerking moment. Unfortunately, the game is Japanese without subtitles, so it can be hard to pick if you haven't read a translation. The entire tone of the game is rather sad, what with you being the last remnants of the human race and all. But the moment where Gai does his Heroic Sacrifice had this troper tearing up.
What's saddest for This Troper is the fact that Creator was never able to tell the clones of Buster and Leana about the Stone-Like and change the future. All he did is create a Stable Time Loop and humanity can never be saved.
Unless you count Ikaruga as in the same universe......