Known as the Goemon series in Japan, the Legend of the Mystical Ninja games are highly popular over there but only managed a small cult following in English speaking countries. A lot of that probably has to do with the game's quirky and distinctly Japanese humor, and the fact that the main premise of most of the games is of traditional Japanese culture trying to fight off Western influence. Four of these games were released for the Super Famicom, but only the first was translated to English and brought over to the Super Nintendo. It deserves more attention than it's had, as it's a very colorful and fun side-scrolling action game with a really good soundtrack.
This one gets off to a silly start and maintains that tone through the rest of the game. Some ghost chick has invaded the nearby Horo Temple and has been turning people into monsters, so Kid Ying (a young ninja who looks like he's wearing some sort of dead animal on his head) and Dr. Yang (older perverted gentleman with braids of hair running up into his nose) take it upon themselves to set the situation to rights. This leads into some long and intricate plot involving ninja cats and saving the world and all of that.
There are nine levels, each of which is basically centered around some sort of town. In town, you move around on a 3D plane (think Double Dragon or River City Ransom) while a never-ending wave of various and assorted assholes constantly comes charging along looking to do you harm. Hitting them causes them to drop coins, which you can spend in various establishments around town. They also may drop a cat, which upgrades your weapon to something with more reach, or a scroll, which allows you to use Ninja Powers (once you've purchased them).
There's a tremendous variety of shops and mini-games to blow your money on in the towns. You've got the expected things such as stores that sell armor and food, and inns that recharge your health, but then there's all sorts of quirky gambling and general diversions. There's a dice game featuring some naked dude in a toga, a quiz game where you are asked trivia about previous areas of the game, a simple MS Paint board, a Concentration game, a 3D maze, ring tossing, and probably a bunch of others that I have forgotten. There's also arcades in a couple of areas, which allow a solo player to play the first level of Gradius, or two players to go a round of Pong or Blades of Steel. Usually at some point in each level, you enter a side-scrolling area (the gameplay doesn't really change but the third dimension to move in is eliminated) which culminates in some sort of a big boss fight.
I think frustration was probably the biggest thing that kept people from this game when it was originally released. You are basically under constant assault at all times except when you duck into a shop, and taking even one hit means you lose your weapon and upgrade items (such as the sandals that make you move faster). The later stages are really pretty unforgiving, and the password system to continue is one of the longest I've ever seen. Well, at least one of these things has been improved by modern technology - playing on the Wii you can use the native save function, as you would on an emulator. I think the game is worth the effort, especially for two players. Colorful detailed graphics, great music, great atmosphere, lots of goofy fun to be had.
Thorough article on Japanese cultural references in the game