The reason why I love the series so much is that I have the hardest time ranking them. I like each of them for their own different reasons, so in a perfect world I would say "I like em all the same!" However, I can't do that here, so I will try my best.
1. MGS2; when I first played it, I didn't know what to think and felt betrayed when I was suddenly having to play with this new guy. As time went on I started to realize and accept the brilliance of the story decisions and how Kojima refused to give us more of the same, and instead took massive risks that I felt paid off beautifully. I also love the art direction and general aesthetics of the game.
2. MGS; this one barely squeezes out MGS3 because of nostalgia/memories. The storytelling was awesome, the music mindblowing, some truly emotional moments, and a wonderful ending.
3. MGS3; one of the greatest endings ever in a game, lush environments, The Boss, The End, the Shagohod chase. Incredible.
4. MGS4; I love it, but dislike the in-between act stuff on the plane, how each act has to install, and I thought the final boss fight and setting was weird and poorly done. Not nearly climactic enough for me. However, everything leading up to it was amazing at least, such as the Vamp fight, the Rex vs. Ray fight, etc. That being said I think it's a phenomenal game and a fantastic sendoff for the series.
Hardest thing I've ever had to do GAF. Here's to you.