General:

PC98.org - Constantly-updating database of PC98 software with screenshots and descriptions (no downloads, although they are available by request)
PC-9800 Reference and Link - very comprehensive and useful database of links related to programming & graphics editing on the system
PC98 Emulation Guide - what it says
9800 Guide for Western Beginners - an accessible and concise guide for English-speaking buyers that's not too in-depth as to be overwhelming but tells you just about everything you need to know
Lost in Translation: An NEC PC-98 English Documentation Project - another English blog documenting the process of acquiring and setting up a PC98
第三研究所 - Japanese-only unfortunately, but this site is a lifesaver with too much useful hardware info to list
modelrail.otenko - Has some PC98 related articles in the "retro" section

Downloads:

Neo Kobe on Archive.org - largest single archive of games on the web
Vector - massive freeware/shareware site that contains games and utilities for older systems including PC98
PC-98愛好会.NET - the 固定ディスク section hosts user-uploaded utilities, MAG images, homebrew games, etc.
FMP Music Disks 1-9 +α on Archive.org - tons of PC98 music files

Music:

pedipanil's guide to MML - Very accessible and easy-to-follow guide on PMDMML, a text-based markup language that was commonly used for composing music on the system

Technical:

NEC PC98 Basic Reference - (English!) some indepth technical articles about the hardware
PC-98用拡張ボードのスイッチ設定 - dip switch settings for different expansion boards
Project M.P.S. Japanese-only site focused on doujin hardware, but has a lot of good info about how to get SCSI drive emulators like RaSCSI and BlueSCSI working reliably on PC-9800

Misc:

TMK NEC PC98 Keyboard Converter - dongle to use a PC98 keyboard on modern Windows
PC98 startup beeps compilation
HTML まぐろーだー - browser based MAG image viewer, just drag and drop into window
Polestar papercraft - an official papercraft file of the car from Polestar made by Bio 100% as a bonus for a box set of music cds... i just thought it was cute

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