LINKS
Three Steps to a Reef Aquarium
This is the site that started it all for me.  It's simple and easy to understand.  Though there is more to know about reefkeeping  than just these three steps, this site gives you a great overall view of how simple it is to set-up a reef aquarium.   It also introduces many of the issues being debated in the reefkeeping hobby.  It has been recently updated.
G.A.R.F
What do a bunch of Idahoians know about coral reefs?
Alot,s it turns out.  The Geothermal Aquacultural Research Foundation is one of the best sites on the web to find the most cutting-edge theories in reefkeeping being put to the test.  They are also a great source for "clean-up crew" critters, bullet-proof reef set-ups, DIY tanks designs, and of course that wonderful G.A.R.F. Grunge!
Aquarium Frontiers
I'm still using the old title for this site because it is (was) one of the ledgendary reef web sites.  Originally founded by Terry Seigal and Julian Sprung in the early 1990's, it has always had top-notch writing .  Though it is sometimes over the heads of beginners (go back to articles you didn't understand as you gain experience and they'll make sense), it is a good source for basic and advanced reefkeeping. 

It is now part of Fancy Publication's "Animal Network" Aqauarium site.  New articles are rare.  The archives are invaluable.
About.com's Saltwater Aquariums
Stan and Dabbie Hauter have created the single greatest resourse for saltwater and reef aquariums on the internet.  With links to over 700 sites, you can find nearly anthing related to marine aqaria.  The discussion forum is a great way for beginners to get up to speed on the myths and facts of reefing while joining a great reefing community.

Get on their emailing list, it is well worth it

REEFS.ORG
This is the site of the "big boys".  Most of the members are master reefkeepers with years of experience.  When you have about a years worth of experience reef keeping this is "the" discussion forum to join in.  Untill then, read the articles follow the links and read the forums.
Janet's Reef
This is a great "just a regular reefer" site.  I have learned so much from the articles and discussion board.
Richard Durso's Reefland
Not only can you find many variations on the silent stand-pipe design, but there are other DIY projects that may solve some of your other reefing problems.
John Rice's 450 Gallon Reef Aquarium
This is one huge aquarium, with one of the biggest refugium sumps I've ever seen.  The sump/ refugium is made from a 300 gallon horse troth.
Mr. 4000
So, you think you're a committed reefer.  Meet a reefer who ought to be committed.  A 4000 gallon home reef tank.  What dreams are made of.....
Eco System Aquariums
This is where much of my current methodology originates from.  Leng Si's EcoSystem Method of reef keeping has had more people talking about "converting" than Dr. Walter Adey ever did with his "Turf Algae Scrubber".  Mostly because Mr. Si has produced results rather than just logical conclusions. 

The Miricle Mud is a little pricey, but when you consider that you don't have to buy a skimmer, live sand (for your refugium), critters (for your refugium), or caulerpa (for your refugium), the price is about the same.

Note: I didn't buy the mud, I just "bought" the argument.  If I was starting over, or building a new system I would probably buy the mud.

Though the "method" is little more than a refugium replacing a foam fractioner, this is a big leap in popular reef aquarium thinking.  The skimmer has been the heart of a reef system.  Your tank was judged by the size and efficiency of your skimmer.  In the near future, your success will hang on the size of your refugium.

You have a skimmer?  Wake-up and smell the 21st century.
NEW
Advanced Aquarist's Online Magazine
So far, this looks like the new "Aquarium Frontier".  Put together by the guys at reefs.org and Terry Siegal (founder of the original AF).  The contributing aurthors reads like a "who's who" of the aquarium communittee:

Terry Siegel, Craig Bingman J. Charles Delbeek, Doug Robbins, Richard Harker, Dana Riddle, Randy Holmes-Farley, Julian Spung, Rob Toonen, Eric Borneman,
Frank Marini, Martin Moe, Greg Schiemer,
Randy Donowitz, Sanjay Joshi.

The forum is an extnsion of reefs.org, which means your reefs.org name and password can be used here.
Reef Aquarium Guild .com
This is a great up-and-comming site.  If, like me, you could look at pictures of other peoples tanks all day -- Then this is a great site.  Reef Aquarium Guild takes what is best about other, larger, sites and leaves out the fluff.  Membership numbers are a little low at this writing, but high for the short time it has been up.  I'm sure this site will become one of the largest reef-interest sites on the web.

Great discusion section, member tank photos, articles, and much more.
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