- The NES Forums are back. A message board dedicated to the NES!
NES Guide - Good site with a comprehensive listing of NES games
NES Player - One of the largest and most original NES sites on the net.
NES World - The web's most comprehensive site for information on NES hardware and peripherals.
NES Zone - A long running (but seldom updated) NES site.
paNESian press - A classic NES site from way back
Play NES Flash Games - The name pretty much covers it. This site allows you to play NES directly via the web site.
PlayTheNES - You've probably seen Roth's NES tips videos, now see his site. There are forums here also.
Overclocked Remix (NES) - Remixed music from NES games.
Seanbaby's NES Page - If you've never been to this NES humor page go now. You'll thank me.
Smackdown GT - Smackdown GT, an oldie but goodie.
TSR's NES Archive - One of the oldest (and still one of the best) NES sites around.
 
NES Dev-Related Sites
Codeburst 6502 Assembly Tutorial - A gentle introduction to 6502 assembly programming
Famicom Party - Kevin Zurawel's site dedicated to NES/Famicom programming
 
Partial NES Sites
8-Bit Girl - Game news, reviews, and interviews, including retro content.
Classic Games Blog - Solid classic games blog featuring a lot of NES content
Game List Mania - Site with lists on a variety of gaming systems, including NES.
Honest Gamers - Video game reviews community
 
Commercial NES Sites
1 UP Card - Specialized Game Cartridge Cleaner for Nintendo, Sega and more.
DKOldies - A very solid gaming store featuring a wide selection of NES merchandise.
Good Deal Games - A non-profit, game enthusiast run site with lots of content, including for older systems.
NESRepairShop.com - Offers repair services as well as games for sale.
Nintendo Repair Shop - An exciting new idea among the many NES sites on the web. This is (to my knowledge) the first NES repair website. Good prices make this a viable option for fixing any NES-related hardware
problems.
nintendosforsale.com - An online store selling classic consoles and games (including NES consoles and games).
Still Luv NES - Online store selling a variety of classic games, including a wide selection of NES merchandise
The Old School Game Vault - Online store selling a variety of classic consoles and game, including NES.
TriForce Gamez - Online store with NES games and accessories.
Video Game Chest - Online store offering a variety of games (including NES) at a reasonable price.