Dad dying in the purifier.
Amata telling the wanderer if she ever see's him/her again, she'll "kill you".
As I recall, my response was to shoot her in the face.
Spoiler Being shanghaied into the Brotherhood of Steel, and subsequently having to annihilate Adams Air Force Base.
Seriously. It's either join the power-armored boy scouts, or be a dike and get no reward for it.
There is no middle ground. I must have hovered over that console for ten freaking minutes during Broken Steel, going "Yes? No? YES? NO?!"
Spoiler I would have dearly loved to have just disabled the stupid orbital strike platform, so that neither group could use it. Problem solved! Equilibrium achieved! BUT NOOOOO.
...Yeah, I'm a little sore about that ending. Don't mind me. >.> *ahem*
This.
Hopefully you are now enjoying FONV with it's varied choices and moral ambiguity.