For this list, I've imposed only two rules: The games must still be fun to play today, and only games which were commercially released during the NES's heyday are considered. That means no pirates, ROM hacks, bootlegs of unreleased titles or contemporary homebrews are eligible.
Shoot-em-up style games were already a pretty well known genre well before the NES hit the scene, and it continued to get quite a few throughout its life, with a lot of them being unremarkable ports of arcade games with pretty basic gameplay and minimal variation, so I tend to glance over a lot of them. Sqoon is a relatively early one for the NES, but its design is anything but basic - there's quite a lot of mechanics that you'll have to juggle to get far. There are the usual waves of giant enemies to blast away for points, but other sea life appears too - orcas are harmless to you, but will eat up any people you blast free by bombing buildings, crabs drop gold bricks you can collect and turn in for points, and the odd sea slug will drop a magical necklace if you bomb it enough times, which grants a 1-up and a chance at a bonus stage. In between all of this, you'll have to free captured humans, touch them to bring them aboard, and once you have nine of them, drop them off on the "floating island" that appears (one by one, with the B button), which is the only way to replenish your constantly dwindling oxygen supply and gain powerups to upgrade your weapons. The aforementioned gold serves as a more efficient means of doing this - all you need is one live human and a gold brick to get the island to appear again, though this will only refill your oxygen and not upgrade your weapons (which makes it a better option when you've already hit max upgrade). Sqoon is chaotic and outlandish even by shmup standards, but undeniably unique and quite a lot of fun once you get into the swing of it.
114. Marble Madness (Atari/Rare, 1989)
113. Lode Runner / Super Lode Runner (Hudson Soft, 1984-1987)
112. Kyatto Ninden Teyandee (Tecmo, 1991 in Japan)
peripheral that allowed it was never brought over and Nintendo never implemented an alternate option). I did consider including it on the list, but after playing the Famicom Disk System exclusive VS. Excitebike, I can't do it in good conscience. The quality contrast between the two versions is night and day - VS Excitebike includes a more exciting single-player mode (having to qualify for time in a solo run before you're allowed to run a race against the CPU) two player competitive play, music during gameplay, and the ability to save custom tracks directly to the disk. It's criminal that this version was never localized until the Wii U rolled around, as it makes the original game look terrible by comparison!
The original Mario Bros. one gets a lot of flak from retro and modern gamers alike, and I'm really not sure why. Sure, it hasn't aged quite as well as the legendary sidescrolling platformers that succeeded it, but it's still a pretty entertaining game in its own right. Bump enemies, dodge fireballs and icy floors, collect coins, shove player two into that enraged shellcreeper coming for your blood, rush for the panic POW block when things get too crazy... what's not to love here? It's easily among the best of the black box era games, if nothing else. Hell, it even spawned a pretty fun little two-player competitive minigame in Super Mario Bros. 3, so it must be good!
(There is also an enhanced advertisement-laden update on the Disk System called "Kaettekita Mario Bros" if that's your sort of thing.)