I haven't gone through the entire thread, but I'm sure Leap Of Faith has been mentioned before. A huge tear jerker that one.
Also, in DMD when the MC travels to D's town and they are reunited, that scene is so emotional. I definitely cried.
In Callisto, there's a scene where there's a pretty brutal attack on one of the tribes, and Kara's maternal protectiveness kicks in when she tries to save a young alien child. That scene is emotional, too. *edit* - Well, I feel compelled to add that she DOES save the kid and there is a heartwarming scene in the end, but still emotional all the same.
Now & Then is also full of emotional scenes that can make one teary-eyed.
Another one is Avalon. I basically lost it when the Chinese shrink was introduced. Such a beautiful scene.
And then there's Acting Lessons. There are some pretty emotionally intense situations in that VN.
But then, I guess in my old age, a lot of things/situations can make me cry these days. It's getting worse, too.