Easily MGS for the PS1. There was nothing like it when it was released. It had the greatest boss fight in the series (Psycho Mantis), Kojima used the dual shock and memory card in creative ways (hell, he even used the back of the actual game case to hide one of the radio frequencies), and the story was the most cohesive in the series.
For me it's MGS>MG>MGS3>MGS2>MGS4. I was so disappointed in part 4. There were a couple of great moments, but the game came off as more fan service than anything (and not a good attempt at that). It tried to hard to be everything for everyone and forgot why people played the game in the first place (Stealth Action Gameplay). The Drebin system rewarded you for going on massacres, all the emo crap got extremely annoying after the first couple of hours, and the ending cutscene seemed like it would never end. Oh, well...here's hoping MG Raiden gets thing back on track again.