These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Logic: Snake's sneaking suit looking blue made sense in Metal Gear Solid: the landscape was bluish-gray, after all. But why is he wearing the same suit in the very green jungle?
Nightmare Fuel: Marionette Owl's dolls. They are made out of various body parts of his victims. According to him, Snake's clavicle and femur bones would be good to use.
Owl again. He reveals to Snake that when he was 12, he found the remains of a friend of his named Laura, dismembered, disemboweled, and spread into a field. The event gradually turned him insane and he re-lived the moment of discovery every night in his dreams.
And then there's his death, where he realizes he's going to hell:
Marionette Owl: No! NO! PLEASE! You can't-!
What Do You Mean, It's Not for Kids?: Ghost Babel was rated E, the only Metal Gear game to have received less than a T rating during the lifetime of ESRB. The only visible sign of this rating is switching Snake's ubiquitous cigarettes to a "fogger" gadget. Aside from that, this is very much a Metal Gear game with its gamut of Dark and Troubled Past and Ax-Crazy antagonists. To list a few: the backstory for the entire setting of the game includes ethnic cleansing. One of the support characters (Weasel) is reputed to have killed his own brother, which resulted in his mother committing suicide and his father attacking him with a knife, which in turn landed the father in a wheelchair due to a case of excessive self-defense. One boss (Marionette Owl) is a serial killer who builds life-sized dolls out of his victims, tells how he found his female friend murdered and dismembered as a child, and goes to hell as Snake watches. Another boss (Pyro Bison) gleefully describes how he enjoys watching people burn, and kills himself by self-immolation while in the throes of orgasmic joy. Not to mention Snake and Colonel discussing liquor preparation in the prologue and numerous instances of Christ and the Lord's name being taken in vain. Rated E for Everybody, folks!