It's my favourite out of the series too, followed by the original and then the Twin Snakes remake of the original (although I liked the gameplay enhancements from MGS2, the clip scenes to me seemed way over the top and slightly ruined the atmosphere). Snake Eater had a fantastic story, good cut scene-gameplay ratio IMO and easily among the most memorable boss fights I have ever played in a game.
I was heartbroken when my disc broke last year, and therefore am eagerly anticipating the 3D port next year