The following commercial links deal with companies I have dealt with, in one manner or another. You'll find my opinions of them in their entries. All are positive, with the exception of Aquatic Connection (which I list only as a warning). There are of course many other commercial reef sites on the web. I prefer to list only those on whom I've formed an opinion.      

 

Reefkeepers List
www.mjcrealm.com Home of the Reefkeeper's Mailing List. Started by myself, Nathan Cope, Jon Simmons, Jimmy Chen and Branden Culp. You can sign up for the list or read extracts from prior posts here at this site.

 

Commercial
Flying Fish Express: FFE is a fairly reputable mail order dealer who has quite good prices on live rock. Although they have (on the whole) a good reputation, common complaints against them are that their rock is frequently barren of all but coralline algae, they are prone to making substitutions, and they take forever to answer their email. Still, worth checking out both for their prices and because they do sometimes get some truly phenomenal pieces of livestock.
Jeff's Exotic Fish: Jeffrey Majdali is a pleasure to deal with, I buy from him regularly. His prices are excellent, as is his reputation. His fiji rock is very high quality. He offers many other items then what's on his website, so it's worth calling him with specific requests. If you live in Los Angeles, this is THE guy to buy from -- no shipping charges if you go to make a pick up.
Reef Fanatic: Another good company, RF sells livestock and dry goods. 
Marine Depot: Ken Wong (formerly of Reef Fanatic) works here these days. I have not yet dealt with the company, but if Ken's affiliated with them I'm sure they have high standards.
Premium Aquatics: Another livestock/dry goods company with an excellent reputation and good prices. They seem to be slow about updating their web page lately.
Aquatic Connection:  The aptly nick-named "Aqua Con" recently instigated a scare about a new ban on coral collections. The information they provided to customers was wholly inaccurate and misleading. Worse, they have yet to even print a retraction. When I emailed them asking them to verify their claims, they replied by comparing me to those who would have nothing to do with Jesus Christ (for doubting them). You give them your money if you wish. I certainly won't be.
Thiel Technologies: I list Albert's site as commercial because he has a members only library that one must pay a yearly fee for access to. Nevertheless, most of the huge amount of material on his site is free, and he maintains a Reef mailing list which is very popular. Worth bookmarking.
Aquatic Lighting Systems:  ALS is the manufacturer of those $75 metal halide kits that are advertised in FAMA magazine. Jeff Katz (the owner) is a pleasure to deal with, and his products exceed expectations Take a look at his products, as they really are a good value. (*DISCLAIMER: I am affiliated with ALS, inasmuch as I was hired to build a web site for another of Jeff Katz' Companies [not ALS]. I do, however, actually use one of his halide fixtures).
G.A.R.F. The Geothermal Aquaculture Research Foundation has a thing for cutesy acronyms, but on the other hand has noble goals. This site is primarily educational, but they do sell a few products (including their well-thought-of Janitors) via mail order.
Custom SeaLife: Makers of reef aquarium Power Compact fixtures. The page on their SeaLights fixture is particularly useful for Nano keepers. (Btw, I've got a flatback hex tank with built-in wet/dry like the ones they have photographed on the SeaLights page. Mine is for sale. Email me if you're interested).

       

Personal/Organizations
#Reefs.org:  Primarily dedicated to providing a reef chat room with scheduled speakers, this site has a little of everything.
MASLA The Marine Aquarium Society of L.A will be hosting MACNA this september. If you live nearby, I encourage you to join.
Fish Information Service (FINS): An excellent reference archives site, it contains (amongst other things) the marine reef FAQ.
Jeff Pfohl's Archives: This site houses an archived collection of threads from the various marine aquaria newsgroups. Quite simply, bookmarking it is a must. It's invaluable.
Aquarium.Net An on-line reef magazine, it's most notable for the mailing list it maintains. The list of eminent contributors to both the magazine and the list is quite long.
Micro Reef Aquarium Some very sparse info on a 10 gallon micro reef. It has pictures, though :)
Fernando's Fun Topics Another site with sparse info on a 10 gallon micro reef. No pictures, though.
Branden Culp's Page Branden is another reefkeeper dedicated to Nanos. His site is still very much under construction, but should be very useful once completed. I get all tingly because he has me as one of his "Top Picks" links.