:|....I always hear about this and I never liked the idea...Mostly because Kojima shoehorns religious iconography when it suits him. I saw this years ago in a early MGS4 trailer https://www.youtube.com/watch?v=gyfE04MI7-Q they obviously cut it out because it has no context...just liquid babbling on.

Then I found this http://tvtropes.org/pmwiki/pmwiki.php/Main/FauxSymbolism

"Metal Gear Acid 2 names the Test Subjects (Golab, Harab Serap, Chagadiel) after the Kabbalist Qliphoth for no good reason, and names the Metal Gear Chaioth Ha Kadosh (host of angels) and gives it a choral piece as a Leitmotif.

The opening scene of Metal Gear Solid 2 shows Snake (who had at this point abandoned his dream of having a normal life in order to fight against Metal Gear proliferation, as his 'duty to the coming generations') throwing himself off a bridge with his legs together and his arms outstretched in a wide crucifix pose. He's in Active Camo at this point, so the effect is made even more extreme by the fact that all that's visible is the outline of his long-haired, nearly-naked silhouette. Oh, and an ethereal choral song plays as he does it. For a while during development, it would have been more extreme, with Snake wearing a brilliant white parachute that would spread out behind his body like a pair of angel wings. A lot of the symbolism is mollified, though, by the fact that when he lands on the surface of the Tanker there's a big Homage Shot to, of all things, Terminator.
Metal Gear Solid 3 is considered by many to be a major offender, with codenames like ADAM and EVA, Snake, and biblical comparisons in the ending monologue. Likewise with Part 3 of Metal Gear Solid 4, where a discussion of the events of MGS3 takes place in a church and adds a very symbolic apple to the mix. It a more meta-symbolic sense, there are many easy-to-miss references to the earlier games, to the point where at least one analysis speculated that the way certain eggs in a loading cutscene cook represents earlier characters and events. "