Super Metroid IMO. I dunno, just facing a boss that was 2 screens big (no exaggeration), bosses that wouldn't show up for like 15-20 seconds, then barrage you with attacks suddenly in the air, plus the whole Alien movie atmosphere really made Super Metroid stick out for me.
SotN was no flop though. I remember it being ranked higher in some gaming magazines for game of the year than FFVII, and that's saying a lot!! Plus it's soundtrack is so B.A.D.A.S.S!! I still listen to some of it's toons to this day.
They should have ported the OG to the DS!!