There was a Super R-Type 2? Chrono Trigger was good if perhaps a bit overrated. The story wasn't amazing or anything. Super Ghouls n' Ghosts just feels so crippled compared to regular, run-of-the-mill un-super Ghouls n' Ghosts (too slow, can't shoot up, etc).
Super Turrican 1&2
I liked the music, but that's about it.
Contra 3
Definitely good, yes, but it's not one that really sticks with you.
Yoshi's island
Maybe this is one of those games that you need to play for a while to appreciate, but I really don't like it. The worst sound in the entire world is that of a crying baby and this game has it in spades, decreasing the enjoyment substantially because of that sound effect alone.
Donkey kong Country series
Ug. The first game was kind of cool, but I really did not like the graphics. The music is even worse (but the underwater theme is awesome).
Super Aleste (Space megaforce)
I still haven't played this game, but I hear it has Blazing Lazers Diseaseā¢ in that is has super-long, boring levels full of nothing.
Lufia 1&2
I may have rented Lufia 1. I don't really remember anything about it. The one thing that pops into my mind, however, is that it had good title screen music. Does it? If so, +1 rep to my memory.
Megaman X-X3 (although not saying much at this point)
I really don't like any Mega Man games besides part 2.