Do any of the current crop of Intel-based emulators support PC-98? Neko Project II looks like it did, but it's still carbon/cocoa. I've been introduced to the Touhou series and it would be great to play it without booting over to Windows...
Looks like MESS supports several computers in the PC-98 family, but only at a "preliminary" level.

Might be worth checking QEMU. Otherwise it seems like you'll have to boot into Windows or run emulation within emulation.