Here are a few links to start out with - we'll have a lot more up soon!

American Science and Surplus - why not visit our neighbors?
Anime Turnpike - (finally up again!)
Animerica - A good website for a good anime magazine!
Arsenic Lullabies - Make sure you're armed with a twisted sense of humor for this comic!
Clone-Army.org: Home of Tomoyo42's Room, as well as a whole bunch of art sketches, song paradies, and online comics!
Comicon.com
Comic Book Resources
DC Comics - Duh.
Diamond Comics Distributors
Ebay.com - Where John wastes all the store's profits... just kidding!
Gamefaqs.com - For all of your video game needs!
Google.com - The Lostwonders.com search engine of choice
Ibox Publishing - The Publisher of Thieves and Kings, one of John's Faves!
Marvel Comics - again, Duh.
Megatokyo.com - "Relax, we understand j00." A great online comic! Go there and read!
RPGFan.com
RPGamer.com
Sequential Tart
Strangers in Paradise Official Website - The comic that everyboby should read (hint, hint, Kelly!)!
Wizard Entertainment - get all the info on all Wizard-sponsored events - like WizardWorld!
Wizards of the Coast - Makers of Magic: The Addiction..., er, The Gathering. They also print a game called Dungeons and Dragons - not that anyone really plays that or anything...
WizKids.com - makers of the ever-popular MageKnight and HeroClix. Mechwarrior is also pretty popular, I hear.