Y U NO LIST SNAKE'S REVENGE!? Haha, I know, not a real Metal Gear game. I have a friend that likes it though so if anything, it may have held up well as it's own game and not a bogus MG tie-in.
I'm surprised Snake Eater is in the lead for being the least best-selling of the Solid games but, yeah, I liked it too. It's my #2 MGS game in a tie with MGS4.
My favorite will always be MGS1, everything about it was just right and it came around at the right time. Before that, my favorite was the original Metal Gear... sadly it had to be the NES port that lost so much of it's original elements from the MSX version.
It's hard though in these days for me to go back and play MGS1, it's just sooooo ugly like all 3D PSX games. Thank the gods for the Twin Snakes remake on Gamecube.
Just as a side note: I really would love to see Kojima re-imagine the original two MSX Metal Gear games with a full script and modern HD presentation. So much remained to be said in those games as still being part of the overarching timeline, I just feel like they should be brought up to date to better match the Solid games.