"People's values change over time. And so do the leaders of a country. So there's no such thing as an enemy in absolute terms. The enemies we fight are only in relative terms, constantly changing with the times." - The Boss, MGS3
"Today's ally may be tomorrow's bitter enemy. Or worse: the time may come when soldiers of the same country will kill their brothers, just like you are now. Who of you can say that tomorrow you won't be aiming your rifles at your neighbors? Your comrades? Your families? Is there no one who has a grudge against you? No one who mocks you? No one who really needs you? Is there truly no one out there who would kill you?" - Gene, MGS: Portable Ops
I've only ever played three MGS games: Snake Eater, Portable Ops, and Peace Walker (in that order actually). I have to say the series has some incredible quotes and philosophy on war and what it means to be a soldier.