I think MGS 1 was best by far. The bosses were awesome, and I liked the no-first-person-aiming-gameplay.

MGS was... well... the worst of the 3 in my opinion. Most of the bosses were ridiculous, and the intro-part with snake was the best part of the game. The katana was cool though.

MGS 3 rocked. Not as good as mgs 1, but still awesome. The End sniper-battle was thrilling. The storyline was a bit primitive though...

Haven't played any of the handheld MGS's yet.