This thread will serve as a compliation of useful links for commander players, both to other sites and to threads and forums on MTGS. If you believe a certain page should be added to it, please PM one of the commander mods or post on one of their helpdesks.
The Magic Rules Resource Page - Contains links to the comprehensive rules, set FAQs, the DCI Document Center, and anything else rules-related you could possibly desire.
mtgcommander.net - The official Commander website, containing formats rules, the official banlist and forums.
Commander Rulings FAQ - Information and FAQ on the banlist, the rules, and a few rules committee decisions that are not necessarily enshrined in the rules themselves. Knowledge of some of these pieces of information is almost essential, so huge thanks to d0su for coming up with the idea for the thread and putting it together and cryogen for currently maintaining it.
How to build a Commander deck - An excellent guide by Blackjack68 that covers all the basics of building a Commander deck, lists lots of commonly used cards to fulfill certain functions, and does plenty more besides. A must-read if you are new to the format.
Gatherer and magiccards.info - The two major card search engines. The former is the official Wizards one, and the latter is operated by our very own Hannes. Which one you go for is pretty much dependent on personal preference. Expect to make heavy use of these when you're trying to find the perfect cards for your deck.
The Decklist Database - Contains sorted links to almost three thousand (and counting) Commander decks built by MTGS users. A good place to start when you decide to build a certain deck - see what everyone else is doing with the general! Many thanks to KingChewie for all his hard work maintaining and updating the database until August 2012, and Dm225 for taking it over until 2013. Scoeri currently maintains this thread.
The Top 50 Cards list - A list of the fifty best cards in each color (as well as multicoloured, lands, and so forth), as carefully chosen and deliberated over by the users. Thanks to Surging Chaos for maintaining the list for several years and DalkonCledwin who created the list. The current list is maintained by the commander moderator team.
Format Staples - A similar list of commonly used cards, compiled and maintained on the official forums by onlainari.
List of Multiplayer Primers - Primer threads are some of the highest quality threads on these forums for discussion of building around each commander. This thread is the definitive list of multiplayer primers.
Cockatrice - The best free online Magic-playing program. No hard-coded rules support, but it's a pretty great sandbox and deck testing resource. Officially discontinued after Wizards got a bit grumpy, but downloads and servers are still hosted by a third party.
Magic Workstation - Used to be the default free online client until Cockatrice showed up.
mwsgames.com - The official MWS resources site. Contains masterbases, themes and documentation, among other things.
Banlist Discussion - If you think card X should or shouldn't be banned, talk about it here. Note that this thread only covers the official banlist. To discuss the French or MTGS banlists, please use this thread.
Sleeve and Deck Box Discussion - Finding a box to hold 100 sleeved cards and sleeves that will last for years can be tough. Here is where you can make recommendations and find suggestions for card storage. Contains a list of relevant products compiled by OmniDreamer.
The Pimp Decks Thread - Got an all foil, foreign, and/or altered Commander deck? Here's where to show it off.
The Looking for Group Thread - Used for locating other players in your area or letting others know where you are in case someone else needs a playgroup.