T98-Next is one of the best PC-98 emulators out there. It works very well out of the box and doesn't seem to need much configuration to get it to work well. The downside is that it's a CPU eater and hasn't been updated in 20 years.
Anex86 is an emulator for the Epson PC-98 clones. It's a pretty popular choice, but keep in mind that its emulation may not be as accurate due to the hardware not being the same. It also requires some pretty hefty changes before running to ensure a decent experience.
Neko Project II is one of the more popular emulation choices for the PC-98. It comes with a handful of different programs for different systems. You'll generally want to use either NP21 or NP21NT. Both work, but NP21NT is designed for more modern Windows systems.
Neko Project 21/W is a version of Neko Project II that works more with the later models of the PC-98 series. It works fine with games for the older systems (I've never had an issue), though, so there's no harm in trying this one, too.
Neko Project II Kai is a version of Neko Project available as a Libretro core, and is therefore compatible with iOS and Linux devices. It appears to be the most complete version, as my friend who uses it didn't seem to be missing many BIOS files.
This guide is mostly geared toward the Neko Project II series of emulators. If you're using another emulator, you might want to look somewhere else for help. Sorry! (I am, however, open to adding information for T98.)
So, you want to play PC-98 games! Lucky for us, there are a lot of emulators for the system floating around online. The most commonly used one is Neko Project II—however, there are multiple versions of it that might suit you better. That, and while NP2 definitely works out of the box, there are a handful of things people suggest you do before you dive in. That's what this page is for! There are multiple guides out there, but I wanted to talk about some stuff I wasn't even completely aware of until well after I got into PC-98 emulation.
To my recollection, NP2 doesn't often come with all of the files necessary for every game. The only exception to this rule is NP2Kai, probably because it's made for RetroArch and Linux. For most games you won't run into an issue, but some older games that rely on BASIC mode or other random pieces of the system might not run.
Go into your emulator directory and check that you have FONT.ROM and BIOS.ROM. If both are present, good! You shouldn't run into any issues. If either are missing, some games won't run (BIOS.ROM) or text may not show up properly (FONT.ROM). Some versions of the emulator may also require FONT.BMP, but I've personally not run into that issue. NP2Kai requires it, though.
Other files you may need are ITF.ROM, SOUND.ROM, and D8000.ROM. I don't know what these do, since I wasn't aware of these files until my friend sent them my way. Additionally, in order to have proper drums in Touhou 1, you'll want 2608_BD.WAV, 2608_HH.WAV, 2608_RIM.WAV, 2608_SD.WAV, 2608_TOM.WAV, and 2608_TOP.WAV. These files are completely unnecessary for the function of the game, however, so it's no big deal if you don't have them.
Finally, you've gotten everything set up, and you're ready to play! You put in a copy of the Touhou game of your choice and—Woah! This runs like absolute ass! Why is everything so slow??
NP2 starts out with pretty barebones settings for its CPU and other hardware emulation. To fix this, go to Emulate, and then Configure... to access the menu that changes all that stuff. You can make it whatever you want, but these are my personal settings:
If you plan on running any Touhou game, I would recommend this as a minimum. LLS' bonus stage may require just a little more speed to run without too much slowdown, but this works for the rest of them. Additionally, some games may require you to have a less powerful CPU, due to many older games lacking a CPU cap. I would recommend getting deeply familiar with this menu if you're going to be playing games from multiple different eras. To apply your changes, reset the emulator.
To access the GDC clock settings, you'll have to go into the BIOS menu. To do this, hold END on your keyboard while you reset the emulator. you should be greeted with an interesting looking screen:
Press the down key to go to the second option, where you should see GDCクロック at the very bottom. Hit enter to access the menu, then go down change the setting. I don't remember if you have to hit enter to save it, but it doesn't seem to break anything if you try.
Are you like me, playing PC-98 games on your dingy laptop with the barebones amount of keys? If that's so, you might be having difficulty with some games that won't register the arrow keys. Luckily, you don't need to buy a whole new keyboard for this! There are numpad emulators out there that are compatible with Neko Project. Any will really work, but I use this one, since it's simple enough.
The PC-88 (and early PC-98 keyboards) didn't have arrow keys, so a lot of ports to the PC-98 didn't bother to change the controls. The later the game, the less likely this will be an issue, though.
I like to mess with my settings occasionally, just to see if there's anything I like. The only thing I recommend is setting the beeper to Beep high, since it mimics the sound of the floppy disk drives reading and writing. I also have Antialiasing (Light) enabled, since it makes things slightly easier to read. You can play around with a lot of audio and visual settings in NP2, so don't be afraid to try things out!
While many are still only in Japanese, the volume of English patched PC-98 games is steadily growing. Many come already in English, however there are still a handful of games that may require you to patch the game yourself. This is a mostly painless process, and most translators will tell you how to do it, but just in case:
Your patch should have come with this software, if you're using it. Otherwise, there's probably a README telling you where to put the patch files. Place the file to be patched in the main directory and run the software. If Pachy doesn't detect it, you'll have to write its location in by yourself. (Alternatively, don't move the file and just write it in where it already lives.) Confirm it's the file you want and let it do its thing. Done!
Place the original file and patch in the places where it asks for them, then hit 'apply patch'. Careful, because checksum validation is on by default, and it might not always recognize the file if it's not the exact one it's expecting, giving you an error. I can't imagine the file being slightly different somehow would kill your game, but I can imagine this is on for a safety reason. In general, patching a file with a different checksum should be fine, as long as the files it's looking for inside your HDI/FDI are the same.