--Kojima went ahead and made the scene on the bridge with the boss CQC dismantling Snake's gun before consulting Mori. So when he did show the scene to Mori he asked if you could do that. Mori replied, "That's impossible in reality" and Kojima laughed.
--A lot of the live-action footage was shot by Kojima. He said their live-action budget was quite high and you could finance 2-3 eps of a TV show for what they spent. Originally the footage was in color, but he ran a filter over it to make it fit with the real footage.
--The sky diving scene is an homage to Kamen Rider. The mask an homage to The Fly. The scene where Snake walks out with Solokov and the guards are hiding in ambush is an homage to some John Carpenter film. The scene at the horse with Big Boss when they fight is an homage to Ashita no Joe.
--The food eating is according to Kojima like an Asoep Fable. The Japanese name is aritokirgirisu (the ants and the grasshoppers) [not quite sure how this fits in as I don't know the story]
--Ocelot's style of shooting in the VM part is actually a real tactical style. Only the blowing off the gun at the end was added for cinematic effect.
--The movie trivia was written by Mura Shou and Kojima himself swears he doesn't watch monster B-movies
--Kojima really wanted Carl Weathers for Volgin. He loved him in Predator and personally asked him to play the part to which he accepted.
--When doing the motion capture for the Snake Eater landing scene where Snake rolls around. Kojima wanted it to be even more violent with Snake being flipped and smashed around but the motion actor said something to the effect of "I'm not getting any more beat up"
--The motion actor for Ocelot made up all his gestures on the scene and Kojima liked them and used them all.
--Kojima imagined The Boss as Charlotte Rampling in the beginning.
--Kojima said The Boss's suit was inspired by "Annu Taiin"
http://paranoia.on.arena.ne.jp/k-7.html
--The idea that you can destroy the food supplies and weapon supplies was brought about because Kojima remembered a gun shooting game he played a while ago where when you'd destroy an enemy base in the background the amount of soldiers would lessen.
--Kojima original wanted a whole different OP sequence if you chose the Raiden start with completely different lines that were goofy and girly and more Raidenish. But it was cut due to time and disc space.
--The bike scene with Eva taking out Ocelot was actually done in motion capture. It took them a long time to pull the flip off but they did it.
--The gun maniac scene was written by Shinkawa, Hirano(sp?), and Toyopi.
That's most of the trivia facts where I am in the book (right before the Ocelot fight). The book is like an audio commentary in book form with the majority of the game transcripted and Kojima adding in comments every 2-3 lines.