I am going for Super Metroid because, like Yoshiman said way back up there, it is just so fun to sit down and play. I mean, it is just one of those games where you can sit down and play it, even if you don't feel like playing it, you get into it in a matter of minutes. Not only is it one of the best Metroid games I have played, but one of the best games overall.
I would have to say MZM comes in a close second, it was a fun game. Metroid Fusion kinda dissapointed me, but it was still fun. MP was a great game, just not my favourite. MP2, I am still in the process of beating it...I got it for Christmas, and haven't beaten it yet. I don't like it at all, really. It kind of sucks if you ask me. I have yet to beat Metroid, and yet to even play Metroid 2: Return of Samus.