There are a lot of cool websites out there related to MTG and they're all useful at one time or another, but here are the ones I especially love or have found the most useful:

Ralph Herold's -- Magic Library

Originally Bob Flaminio's Magic Rarities, curation of the library has since been remanded to the excellent skills of Ralph Herold. This website is a terrific resource if you are trying to find arcane MTG obscurata on little-known magic rarities. Apart from just rarities, the site includes an almanac of card sets, detailing exactly which sets were available in which languages.  Finally, and perhaps most useful, is the excellent Magic Library Discussion Forum wherein you will find contacts for all your obscure collecting needs. 
 

Brett Allen's Guide to Identifying Non-English Magic Cards

Brett's page is very helpful at distinguishing the hard-to-differentiate Asian and European languages and can save you a lot of time determining exactly what language your non-English card is printed in.
 

The Magic Online Trading League

If you call yourself a magic trader, and you're not a MOTL member, you're really missing out on something special. Traders from all over the world come here to discuss magic or things in general, to post have/want lists, to hold auctions, to read and write articles on deck construction and other topics, to get ruling and pricing data and just about anything else you can think of. At over 25,000 members, this is a resource that shouldn't be overlooked!
 

MOTL -- Price Lists

Worthy of it's own mention, this portion of MOTL will allow you to get a price for any MTG card (foil or otherwise). These prices are based on statistical analyses of completed eBay auctions (i.e. REALITY) as opposed to anyone's personal opinion. They are a great neutral source for pricing information.
 

MOTL -- Rulings Search

Find the very latest rulings and errata on any MTG card, instantly!
 

Crystal Keep

Rulings, set information... all kinds of groovy information. Definitely worth bookmarking.
 

MTG News

A great news resource for Magic: the Gathering.
 

Squt's Magic Misprint Page

A truly impressive attempt to document all known MTG misprints, world-wide.
 

MTG HomePage at Wizards of the Coast

Well duh... no MTG link list would be complete without this one!
 

Gatherer: The Official MTG Card Database

Check this one out, it's an online magic card database maintained by Wizards of the Coast.  You can search on almost any criterion and get all the information about any card including a picture of the card.  Slick! 
 

Magic Suitcase

Although I don't like the direction Magic Suitcase has gone in, and have since developed my own tool for tracking card inventory, I have to give suitcase props, and if you don't use it to track your collection, you should seriously consider it.  Even my new tool still uses a modified suitcase databasen
 

Troll & Toad, Inc.

I got my Summer Magic Stone Rain from these guys. They're a great resource and their online store is very convenient and easy to use.
 

CoolStuffInc.com

I got my Alternate 4th Edition Stone Rain from CoolStuffInc. Good place to go whether you are looking for obscurata or the latest hot tourney cards.
 

Ben Thompson Art

Website for Ben Thompson, Mercadian Masques Stone Rain artist. You can order proofs, prints, and original works through Ben's site.