First, the graded sites, in order of greatness (for more information on these sites, visit my website reviews section):
TSR's NES Archive (96.60) - I'd imagine you've already been here, but in case you haven't, go now!
Old-School Gamer (94.20) - This is a top-notch NES site. Lots and lots of sections. I wish some of the sections had more meat, though.
NES Enshrined (94.20)- No longer updated, this site still is amazing. Great reviews. And just look at those big words Dief uses! My small brain has no idea what the hell he's saying, but it certainly sounds good. (And anybody who likes Ice Hockey is just fine in my book) Note: NES Enshrined is now found on Loogaroo's NES Lair.
Seanbaby.com (94.10) - The funniest NES site. By far.
Tha NES Smackdown (92.90) - An NES site that you're sure to get a kick out of. It's updated again, and has moved to a new location.
NES World (92.60) - It's been around for five years, and the hits keep rolling in. So do the updates. This site has a wealth of information that you can't find anywhere else.
Big Stu's 8-bit NES Wonderland (92.40) - Big Stu's site is pretty good, but I wish it was updated more (it is updated monthly). Make sure to look at Caption NES.
The NES Triforce (91.90) - That's right, it's back. And good as ever.
NES El33t (91.10)- Like Any-S Offline, this site doesn't get as much credit as it deserves. Take the NES Tests, which are found under A Bunch of Quizzes.
The Warriors' Dungeon of NES (91.00)- It's mostly a humor site, and it does get you to laugh. Interviews are also worth a look (damn you Nakoo, I was going to do interviews on my site until I saw that you had them. Grr…)
TNCA (90.30) - There must be some reason this site is approaching 45,000 hits. Go check it out for yourself.
NES Retreat (90.20) - This site was left off of the links page for a couple months. Huge oversight. Go see the comics section, it's pretty cool.
NESfan (89.10) - A site that's got a faithful following. NESfan includes a message board, chat room, and a few dozen reviews. Add in the almost daily updates and I'd say it's worth checking out.
Simply NES (89.00) - A site that you'll just love the first time that you see it. Simply NES has a nice little section on prototypes that I find especially interesting.
Quizzle's NES Page (88.90) - A great site that unfortunately won't be updated anymore. The two paragraphs that pop up when you first go to the site have been read by me countless times. Check it the Spazz Files, with content from the now deceased "Spazzoid's NES Stuff."
Toneman's Page O' HappiNES (88.90) - Although this site no longer gets updated, it's great fun to look at. It was started a long time ago - 1997.
The Internet NES Database (88.40) - If you are looking for game data, a title screen pic, or games by genre, I suggest this as your first destination. INDB would be higher up the list if it weren't for the complete lack of non-textbook content.
Willyman's NES Page (88.00) - I think it was Loogaroo who called Willyman the next great game reviewer. His reviews certainly put most of the competition below him. This is arguably the NES site with the most potential.
Loogaroo's NES Lair (87.90) - One of the best game reviewers ever, Loogaroo also has lots of game show information on his site.
Kid Niki's NES Page (87.60) - This is a super funny site...you'll really enjoy reading it.
This Old NES (87.40) - A site that's newer than mine that has some great, original content like pranks and episodes of the SMB Super Show. Also, it's updated every couple of days.
AntroNES Archives (86.90) - In need of a few major updates - this score would be lots better if it hadn't gone unupdated for about six months.
NES Town (84.10) - Once you figure out how to make it around this site (it has horrible navigation) you'll find that it's alright.
Spreck's NES Place (84.00)- A fun little site. It hasn't been updated since April and is rather small, but some of the stuff is still worth your time.
And now, the ungraded sites. Sites near the top are the biggest ones or the ones I visit the most or have some other reason for being there.
Panesian Press - The newsletter for NES fans.
The Nintendo Game Archive - Do you want screenshots of hundreds of games? Well then…
Goat and Bubblun's NES Wonderpage - I don't actually visit this site too much. (I do like the prank mails, though). The main reason this page gets high billing is the message board.
The Howard and Nester Comics Archive - We all remember these two who starred in the comics in Nintendo Power. This site is completely devoted to them, with scans of all 25 comics that have Howard and Nester.
NESurbia - A site that I just found very recently. The webmaster seems to be intent on creating the largest database of NES manuals ever.
Cl@y's NES Site - The section here that you must see is the NESW.
Andy's World of Nintendo - A small site run by the former owner of the Earthbound prototype. Needs to be updated.
Royal Ranger's NES Site - A very new site that has some potential. Make sure to check it out if you haven't already done so.
EmuNation - The webmaster here has an interesting idea; combining game ROMs with game reviews. Although the site is still new, and therefore small, EmuNation could eventually be quite a site.
Tetrian.net - My friend's site.