Tons of the games were simple shmups, so I can understand people who might have the wrong idea about the library. Also, the library in Japan was way more impressive than what made it to the west. Gekisha Boy in particular still stands out as a fun and unique game (though you can play a translated version on your Mister). Fire Pro 3 is an incredible wrestling game that I still play today (no japanese required). There was another game, Zero4 Champ, which had unique drag racing gameplay (it was all about timing your gear shifts). It was hard to play without japanese knowledge, except for the 2 player head to head races. For CD games, of course, Castlevania: Rondo of Blood is well known.
I actually really liked Jackie Chan's Action Kung Fu. The NES version is pretty ok too, but I think the TurboGrafx version is a bit better. There's also the Bonk games, Air Zonk, Alien Crush, and Legendary Axe: all pretty fun games with good art style and decent controls.
Rondo of Blood was actually the only PC-Engine game I had actually played before the MiSTer, and of course it's a classic for a reason, it's great.
Something I find charming in how utterly incompetent it is is the Addams Family game on the CD. I have no idea how the hell it was even released, let alone made, because it is absurdly bad. You play as the lawyer from the movie (the absolute least interesting character in the movie) and apparently all the Addams' want you actively fucking dead. It's so unbelievably terrible that I sort of got obsessed with it and managed to actually beat it.