Ok, picked up a good few games to get me started. Some stuff I got is on Nes, but I wanted the FC versions due to extra content, or in the case of Rockman 4, because it's cheaper on FC. Going to list what I have gotten so far, and on the list add in what differences I know of on the Fc version.
So far got the following:
Goonies: Not aware of any differences really compared to arcade VS. version.
Rockman 4: Other then title screen?
Akumajo Densetsu: Music, enemy sprites, placement of some blocks, etc.
Karnov: Story scenes have been included.
TMNT (Ninja Turtles 2 Arcade game on Nes): Sprites have been fixed for Foot ninjas, Michelangelo, and Bebop, and soem background objects are different.
Ninja Ryukenden:

Ninja Ryukenden II: Has a ending easter egg, and Jaquio's sprite is slightly different.
Double Dragon III: Easier, and you start off with more energy. There is more ending content also.
Super Star Force:

Spartan X:

Ikari 1: Title screen???
Ikari 2: Title screen and continue code???
Contra: Story scenes and ending, and visual effects added.