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 fuel 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 fuel 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.
A fairly popular game in its time that isn't talked about much these days, Astyanax was quite a sight to behold on the NES. Large sprites with a surprising number of animation frames, elaborate and detailed backgrounds, some imaginative (and gruesome) boss designs, and gameplay slightly reminiscent of Castlevania. The player gets a choice of three weapons, though the way they operate is slightly odd - some get more damage from simple swings but cause the player's magic attack to consume more or less of the gauge in return. A relatively fun game to play through regardless though, and the imagination employed in its visual design alone certainly makes it worth a look for fans of obscure gems.
The Japanese version might just have my favorite Engrishy title of all time, too: "The Lord of King."
If you watched a lot of cartoons in the '90s, you might remember Samurai Pizza Cats - a dub/recut of the Japanese anime "Kyatto Ninden Teyandee" that ramped up the silly humor to the nth degree. I also got into emulation around that time, which led me to learn that there was a game tie-in to the show, so it quickly became one of the very first Famicom games I emulated. It does a good job recreating the feel of the show, with animated cutscenes between stages and before boss fights, several recognizable characters as bosses and recreating most of the protagonists' iconic special moves. Even the Rescue Squad appears, allowing you to traverse various obstacles the main cast can't - punching through blocks, tunneling through dirt, swimming through the water at great speed or even flying for short distances. While not an amazing game on its own, the fact that it captures the feel of the show so well and has such nostalgic factor will always earn it some points in my book.
94. Wario's Woods (Nintendo, 1994)
A relatively unique and well-crafted puzzle game by Irem, where you play as a snowman-esque character named Kickle who can create ice pillars and freeze enemies with his breath to turn them into cubes. Said cubes can then be pushed into the water to create floors, or pushed into other enemies to eliminate them, or ricocheted off of springs or hammers to redirect their motion (though they can easily clobber you as well, so you must be careful). Your goal in each stage is to collect the three "dream bags", though as in any good puzzle game, this quickly becomes a daunting task - avoiding enemies, being careful not to trap yourself and setting up pillars in the right time and place to avoid hazards are all skills you will have to master (especially in the bonus stages, unlocked after completing the main game). There are boss fights too, which require some quick movement and reaction speed to overcome.
91. Arkanoid (Taito, 1986)Another game known for its wacky plot, introducing a wireframe Moai head named "DOH" pulling Earth's space forces into a pocket dimension or some such nonsense. It's all a bit arbitrary, though, since this never comes into play until the final stage of the game; until then, it's all about smashing bricks with a ball and paddle in a game heavily inspired by Breakout. The gimmick that sets it apart, though, is its powerup system - broken bricks drop icons that enlarge your paddle's size, give you multiple balls to break bricks with, allow you to "catch" the ball and release it at a more favorable angle, and my favorite, the ability to shoot lasers from your paddle to break bricks and destroy enemies. The game even came packaged with a custom-made controller that featured an analog knob, which made the gameplay much more smooth than with a standard controller. It's a bit of a scarce collector's item these days, but if you can track one down, give it a go with this game. It will not disappoint!