Beaufort House Index of English Traditional Witchcraft
http://beaufort.bravepages.com/
This family tree of British traditional Wicca, showing the history and inter-relationships between a wide variety of traditions, and with a mini-page on each trad and links to sites by members of that tradition, has now moved to a new host, though it still doesn't appear to have been updated in a long time. Still, there's useful information here.
Breathless Noon
http://www.mothersmagic.net/
First called Amber's Circle of Wicca, then Mother's Magic, this site, created by Amber Laine Fisher, author of The Philosophy of Wicca, has evolved yet again, this time into what the author refers to as "a personal exegesis of holistic romanticist theologies." The focus is no longer specifically on Wicca, though there is still a fair amount of content dealing with that, but on Fisher's personal spiritual journey, which has evolved to draw on Judaism and other spiritual traditions in addition to Wicca. As always, an interesting and thought-provoking read.
Chas Clifton's Writing on Paganism, Wicca and Nature Religion
http://www.chasclifton.com/
One of the very few decent authors ever to be associated with Llewellyn Publications, though he no longer writes for them; Clifton is also an academic; co-ordinator of the Nature Religion Scholars Network, and editor of the International Journal of Pagan Studies. This site contains articles that did not make it into his four Witchcraft Today anthologies due to their "controversial" nature, plus a collection of his "Letters from Hardscrabble Creek" columns which you may have seen in various pagan magazines, and other writings. I especially like "Nature Religion For Real.
CoGweb - The Covenant of the Goddess
http://www.cog.org/
An American coalition of Wiccan groups of various traditions, which is legally recognized as a church in the US and has thereby helped a lot of small Wiccan groups to attain legal recognition there.
Counselling Basics for Wiccan Clergy
http://members.aol.com/JehanaS/c_basics/
Notes from a workshop by Judy Harrow. Absolutely, positively, one of the most useful sites on the web for pagan priesthood of any sort, or anyone else who finds themselves having to do counselling in a spiritual context.
Covenant of Gaia
http://www.cogcoa.ab.ca/
The web site of a Wiccan church in Alberta. Refreshingly fluff-free (no angels, fairies, crystals or Atlantean grandmothers to be found!), and a good introduction to the Craft in general as well as to their specific organization. A nice humour section as well.
Desiree's Musings
http://www.sphinxmuse.net/
A beautifully designed site, though the creative Flash navigation can take a little getting used to, with original essays, book reviews and other resources, most of them considerably more articulate and intelligent than the vast majority of pagan content on the web. I particularly like that it addresses some topics -- like fairy lore and animal spirits -- that are often the subject of shallow, fluffy new age treatments, in a considerably more down to earth and serious manner than you'll find almost anywhere else. Definitely recommended.
New Wiccan Church
http://www.newwiccanchurch.net/
More evidence that traditional Craft is starting to make its presence felt on the web... This is the site of the New Wiccan Church, an association of the various branches of British Traditional Craft (Gardnerian, Alexandrian, Kingstone, and several others) that has been operating since 1973. Their site contains a British Traditional Wicca FAQ, an index of Gerald Gardner's library, and an interesting essay on the historical origins of Gardnerian Wicca, which, refreshingly enough, focusses more on what we don't know than on what we think we do.
Pour Down Like Silver
http://www.candledark.net/silver/
Jehana Silverwing's site, which formerly hosted the Counselling Basics for Wiccan Clergy site (reviewed separately) and still has a link to it, but also contains a number of other interesting articles, including one of the better skewerings of the new age "People don't value anything unless you charge money for it" canard that I've seen ("The Meaning of Value").
The Witches' Voice
http://www.witchvox.com/
Without a doubt, this is the biggest and best-known Wiccan site out there. While there are other sites that offer far more depth, the Witches' Voice is unrivalled for breadth, cutting across tradition boundaries to become pretty much the central nexus for the online Wiccan community, and an invaluable resource for news and networking. Includes special sections for teens, gay pagans, religious rights, and more.
Wiccan Church of Canada
http://www.wcc.on.ca
Canada's first, and still largest, public Wiccan organization, of which I am a priestess. Contains information on classes, rituals and other events in Toronto and Hamilton, plus an extensive FAQ written by yours truly. Due for a redesign soon, now that I've taken over managing it.