It's most definitely Super Metroid. I'm of the opinion that it should be considered one of the best SNES titles, and should be near the top of everyone's top 100 games of all time list.
I didn't play it when it was first released obviously, but it's probably safe to say that no mainstream game had ever attempted its style of exploration-based platforming and had actually succeeded on the level that Super Metroid achieved. Sure, you had other popular games like Castlevania II: Simon's Quest and multiple other cryptic side-scrollers that attempted the same thing, but Super Metroid is vastly superior to all on almost every level. The way it embraces sequence breaking, offers a diversely connected world, and offered incredibly varied gameplay in concordance with the armor/weapon upgrades to slowly stockpile was pulled off in an ingenious manner - the game is among the best speed-running titles for a reason. I fully believe that Metroid needs a return to this type of style, and that a 3DS game like Super would be one of the gems of the handheld library.
A close second would be either Metroid Prime, which seems to be the favorite here, and Zero Mission. Metroid Prime is without a doubt the best 3D game in the series, as it managed to emulate Super Metroid near perfectly while being 3D. Zero Mission would probably be the one I go for with number two though, just because of how snappy and responsive they made the control scheme while, again, maintaining the sequence-breaking and exploration based styles of Super Metroid.
Notable mentions are Fusion and even Prime 3: Corruption. I actually embrace the story elements these two introduced into their respective dimensions, and I hope it continues in the future.
I've attempted to play several of the 2D titles, including Super, and they have never held my interest. I haven't given up on them, but so far the Prime games are the only Metroid games that have gripped me, especially Prime 1.
I haven't played many Metroid games, but I absolutely loved Metroid: Prime Hunters. Friends and I used to spend hours on that multiplayer and it was awesome! Also I really liked the single player in that you almost had the specific target bounty hunters to kill and then you'd get their weapon, thought that was cool.
Noxus was always my favourite
Hunters was pretty good but the control scheme sucked I mean a first person Metroid title without lock on targeting and a bad control scheme that's just sad, aiming with the touch screen would have been so much better with lock on targeting but otherwise its a pretty good game.
I'd put Echoes above MP3. It really didn't add anything the Trilogy/New Play Control Versions didn't aside from Hyper mode and multiple planets. MP2 had tons of Super Metroid references (and even what are speculated to be references to it's inspiration, TLoZ:ALttP), so nostalgia. Yay!
I could see why youd put MP3 above it, given the Hyper Mode feature.