Shamanism: Working with Animal Spirits
http://www.animalspirits.com/
I've put this here rather than under shamanism despite the title, because the focus is very specifically on animals. A very interesting site, with an appealing domain name (animalspirits.com), but slow-loading due to the many animal pictures. Over 300 animals are featured here, with photos and brief descriptions of their spiritual significance. And not just the well-known ones, either -- they've got everything from stink bugs to protozoa! One can easily get lost in here and spend hours looking up different animals, although the academic in me wishes they would cite sources for the historic/factual (as opposed to experiential) parts of the information. In the time since I first discovered it, it's expanded to include discussion boards, chat rooms, and much more. Definitely enough to earn the "Recommended Site" designation, even if parts of it are a little more new-agey than I would have liked...
Feline Revolution
http://www.felinerevolution.com/
A site by two feline therians, divided into personal sites by each of them plus a combined link area. Keller's side of the site, Felinity Reclaimed, contains essays on therianthropy, spirituality, social issues and other topics; poems, and a still-nascent book review section; Kefira's side contains a few essays, some artwork, and several sections that don't yet have much in the way of content, but will hopefully grow in the future.
Akhila's Nest
http://akhila.feralscribes.org/
A personal site on therianthropy, with essays -- often very opinionated -- fantasy artwork, etc. Very attractive design, though the "mystery meat" navigation takes a bit of getting used to. Includes a FAQ on contherianthropy -- that is, therianthropy without the experience of "shifting", where the animal self is present at all times.
Mystic & Anthropomorphic Feline Lore
http://www.lynxspirit.com/feline.html
Formerly a subsection of the alt.horror.werewolves FAQ (listed separately above) dealing specifically with felines, this site is a collection of myths and folklore about various members of the cat family, from domestic cats to lions, tigers, etc. The fact that it's formatted as one long page make it a bit awkward to read through, but it's well worth the effort.
The Werelibrary
http://www.snowspine.com/therian/
A directory of therianthropy-related articles and essays on the web. Fairly comprehensive and nicely designed.
The WEREweb
http://www.swampfox.demon.co.uk/utlah/
One of the larger sites on the topic of therianthropy, with everything from a "were-humour" archive to a listing of European "Howls" (therianthrope gatherings) to articles on Japanese animal lore. Also contains a large index of "werecards" -- little questionnaire-type things that the denizens of alt.horror.werewolves use to describe themselves.
The Werelist
http://www.werelist.com
One of the largest resource sites on therianthropy, offering a very active set of discussion forums, a member database, and other resources.
alt.horror.werewolves FAQ File
http://www.swampfox.demon.co.uk/utlah/Community/fullfaq.html
Those unfamiliar with the newsgroup may at first glance this this a bit out of place in this section, but it's not what its name suggests, or at least not only that. alt.horror.werewolves was originally developed for discussions of just what it sounds like -- werewolves in horror fiction, films, etc. -- but grew into a gathering place for people interested in exploring shapeshifting as a spiritual practice/identity, or spiritual therianthropy, and played a pivotal role in the development of what's now come to be called the therian community. Due to the general degradation of Usenet as a resource, many other discussion spaces on the topic have arisen, from web forums to mailing lists, and pretty much displaced the newsgroup as a community hub, and even the FAQ is now somewhat dated and there's better information elsewhere. But it's stil well worth reading for historical interest, as it was a seminal document in the development of a community.