Never finished Super Metroid. I probs enjoyed Zero Mission the most but I haven't finished that either. Fusion and the X parasites which heal/attack you give it a non-conventional twist which can be annoying I suppose.
Easily Metroid Fusion. I love the power-ups (Diffusion Beam ftw), and it was like the 2nd game I got on the GBA. So I have alot of memories with it. =P I think total... i've beaten it like 20 times, since I keep playing every once in a while. =P