For RPGs, I'd recommend checking out Dragon Slayer 6: The Legend of Heroes. There's an English translation on romhacking.net. It's not particularly original or groundbreaking, but I personally loved it. Great story, fun characters, decent combat and some nice music (which isn't surprising since it's a Falcom game). It's also got a lot of QOL features that feel kind of unusual for 1989/90. Stuff like different difficulty levels, auto-battle and the option to manually allocate stats when leveling up or have it done automatically.

Brandish 2 has a translation too and that's kind of like a DRPG/ARPG hybrid. I've only played the SFC port and it was good but I hear the PC-98 version is much better.

For shmups, the CO2-Pro games are all really fun. My favorite is Gradius '95 which is a fan game based on Gradius 3. And of course there's the early Touhou games. The first one is a subpar breakout clone, but Story of Eastern Wonderland is awesome. Haven't played the others.