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By far the best song in the MGS series is the main theme for MGS 2!
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I think the best songs are Encounter, Escape, and Snake Eater. That includes the Main Themes as well. What can I say? The music is legendary, fit for the adventures in the Snake Legacy!!
My favorite is Snake Eater.
I love everything Snake Eater, but I did oddly enjoy the "Here's To You" ending theme from MGS 4. It fit that sad mood well. Though this may really not count as MGS music, I thought playing that J-Pop music while running-and-gunning guys in 4 was hilarious. Funniest Metal Gear bonus ever.