Super Metroid is still one of the best games ever made. Thet've tried to equal its awesomeness with varying levels of success, but really, Super Metroid was damn near perfect in every possible respect. Visuals, gameplay, level design, boss design, difficulty balance, music, everything. The whole package was picture perfect.
That said, Zero Mission is the second best Metroid game out there. Fusion was pretty good, but I personally didn't like the setting so much, and that irked me more than the extra hand-holding did.
Can you believe Nintendo found a way to make me like a version of the original Metroid? Unbelievable, no?