Battle City - Digdug and Combat had a baby .
Crisis Force -
BEST 8-bit shmup period. Somewhat pricey.
King Kong 2 - Konami top-down beat'em up.
Quarth - Better visuals and music over the GB counterpart released over here.
Sky Destroyer - Taito shmup where you play as a Zero pilot shooting at, presumably, American planes. It's like a slower Afterburner.
Yume Penguin Monogatari - Fantastically Japanese platformer by Konami. Also features shump stages.
Super Mario Bros. 3 - Subtle differences in level design make some levels tricky, and taking damage automatically bumps you down to small Mario. Overall harder than international release.
Ganbare Goemon series - Known in the west as Mystic Ninja
Disk System Games:Vs. Excite Bike - A port of the arcade version to FDS.
Mysterious Murasame Castle - Basically a more linear and action based version of Zelda. Only recently got western release on VC.
Famicom Grand Prix: F1 Race - Similar to R.C. Pro-Am