Most cut scenes tend to follow the same way in the way its made. You have a pro quality all round 3D app to work from, some times (more commonly now) 'extra' apps are chucked in, like Zbrush to add extra details onto models for cutscenes, like the new Splinter Cell has made good use of Zbrush, everything is placed in the scene, animated etc. rendered in their favourite renderer (Whether it be Vray, Yafray, Cinema 4D's renderer, Lightwave's, renderman(pixar's renderer), mental ray and so on) Now you can imagine a high detail scene with Global illumination etc would take ages to render, well most people tend to 'fake' effects that look good, global illumination is usually faked with luminance channels, light domes, baking and ambient occlusion, Pixar has their own solution, make their own fast renderer, known as renderman, using the features at some less quality but much faster results, but last time I looked renderman was pricey.
As for Metal Gear Solid, I think they do their cut scenes real time in their game engine, with MGS 4, they would have obviously chucked in normal maps, shadows, ambient occlusion maps and other shaders to making it look awesome.
Either way, pre-render or rendered real time, both ways are good for cutscenes, I like pre-rendered more, looks nicer and requires less programming
