Maybe it's because I was in my early teens back then but I cried a lot during every MGS game I played. Wolf's death hit me pretty hard as well as Emma in Sons of Liberty, but I was sad for Otacon, Emma can stay dead for all I care.
And of course I cried hard and cursed myself at the ending of Snake Eater, since I had a hard time with The Boss... erm... boss battle. I was really pissed off, calling her ***** and all kinds of obscenities and I was happy when I pulled the trigger. And then there's the debriefing, I learned what The Boss did and I felt pretty shaken up.
Then there's Guns of the Patriots, my own pysch meter went down when Naomi told Snake his FOXDIE was decaying and it would soon make him a walking death machine. And Act 4 was an emotional rollercoaster, all those memories of me playing Metal Gear Solid when I was a kid in that high-tech setting of Shadow Moses, and then seeing it all now, in complete decay, devoid of life.
But the part where I really cried was the microwave hallway, a 42 year old man who's accerelated aging makes him look like he's 70, still struggling, still fighting after all these years, since nobody else can do it. Suffering from the sins of past generations, for the sins of his father. He keeps going just so future generations can a better future.
Then there's the ending, Big Boss appears I go "what in the actual fuck!?" then kills zero and dies, cool story bro. Although it was well directed and struck me.
Since my entire post was dedicated to Metal Gear, I'll share an emotional codec call from MGS1 that some of you may have missed.
When Snake gets captured and subjected to torture by Ocelot, win the first round. You'll receive a call the one that goes like "How's Meryl?" "They got her". Then after you go back to the chamber submit. In the next call Snake will state how he feels like a coward, I think Master Miller even chats a bit with Snake during that call before he ask Naomi to tell him something to take his off the pain.
That call is a foreshadow to Meryl's death, it's a hidden treasure.