Right, so after reading wikipedia, I hunted down three of ID Software games ported to the PC-98, namely Doom (nope, all download links found were down), Doom II and Wolfenstein 3D.

Left is the DOS Doom II, the left is PC-98 Doom II.
However, I ran into a number of problems when running both games. Wolfenstein 3D works ok, but the music was absent (I bet it's the lack of Sound Blaster) and for some reason, any SFX, i.e. the German soldiers death scream - will loop until you make another kill or shoot your weapon.
Doom II is even weirder, regarding the extra space in the bottom. IMO the PC-98 MPU98 MIDI sounds great but the framerate was extremely choppy and at fixed intervals you can hear beeps coming out of nowhere.
Touhou Project games have none of these problems, except that it had a few jumpy frames. Any idea I can fix T98-next?