|ROM Hacking -- Sites about ROM hacking, just like this one here.
Challenge Games -- http://smb3c.darkmazda.com
A good site that has what could very well be the largest hack archive on all the Internet, with 180 hacks from over 50 different games, for 6 different systems. Challenge Games also features "Challenge" hacks of classic games (SMB1, SMB2, SMB3, Metroid, Zelda, and more to come) to make them MUCH harder, yet still fun.
The NIFTY Page-O-Hacks -- http://niftyhacks.zophar.net
This site, made my DarKnight13, features good hacks, such as Luigi And The New Quest, Super Carrots: A New Harvest, Super Carrots 3, and some more. It has also a nice look, featuring carrots (hehe).
RuSteD ROM Hacks -- http://rusted.romhacking.com
BMF54123's ROM hacking site. Its design is nice, and there you'll find Legend Of The Blob Bros 2, Blob Muncher, and some more hacks, as well as BMF's NES Palette, which is a replacement for the NES palette used by Nesticle.
EarthDrake Software's ROM Hacks -- http://members.nbci.com/sirelric
This is Sir Elric's site, which design has been borrowed from mine (with my permission, don't worry) but still looks different enough. There you'll find Chocobo Dragon Warrior, the Quest of Zelda, and EDS Super Mario Bros.
SMB3NQ Homepage -- http://bmcbmc.tripod.com/smb3nq.html
As its name says, this site is about Super Mario Bros 3: The New Quest, which is a very challenging SMB3 hack made by Mr. W.
Hacks in a Sack -- http://hias.briansemu.com
There, you will find many great hacks made by TeMPeS, Big Eli King and Brad, such as "Peach & Daisy" hacks of Mario games, some Zelda hacks, a few graphic-only hacks and some more. The site design is quite nice too, it has nice graphics.
John's Program -- http://71675904jgs.homestead.com/johnsprogram.html
It isn't a really big site, but it has a few hacks, like The 2nd World of SMB3. You'll also find a few NES ROMs there.
Emulation sites -- Other sites related to emulation, but not focused on ROM hacking.
Zophar's Domain -- http://www.zophar.net
This is a pretty popular (and good) emulation site. It has everything (or almost), except ROMs. You need a good emulator? They have it. Looking for hacks and translations? They have them too. And you know there's more than that ...
Bastardly Productions -- http://bleys.ihateclowns.com
It's a site mainly about save state editors ... but there's a lot of various (and fun) bastardly stuff on there, including the Bastardly Forums.
Other / non emulation-related -- Other sites, about misc. stuff, may not be related to emulation.
ExpertGames -- http://www.expertgames.f2s.com/
"With a wide complement of games, cheats, and other diversions, ExpertGames is an excellent place to go if you're looking for something fun to pass the time."