I would have to say Run Saber on SNES, the only game I've ever found that let you change the color of your costume in level. Probably Captain Commando as well (same console), a basic side-scrolling beat-em-up with four characters to choose from (I have never beaten this game). Also Kickle Cubicle on NES, a silly little puzzle game where you can freeze enemies into ice blocks and use the to solve the level. I don't know how niche they truly are, but i've never run into anyone else with a copy.
My true niche game is an arcade game called Goindol. I've only ever seen one cabinet in my life. In the shortest of descriptions, it's a brick breaker game.
In a slightly longer description, it's a brick breaker game with dinosaurs. 🦕🦖 The cabinet has a twist knob instead of a joystick, quite fun.