What a great resource, Karen!

KAK pretty much covered the gamut of the local animal rescues here, but I can definitely vouch for FOSMAS (http://www.fosmas.org/).
I volunteered there for quite some time, and the people there were wonderful.

Some other sites that I had perused when trying to find the right dog for my home included:

Bay Area Siberian Rescue: http://www.bayareasiberian.org/dogsForAdoption.html
A neighbor of mine adopted his two huskies from this organization.

Northern California Sled Dog Rescue:
http://www.norsled.org/

Central Coast Northern Dog Rescue:
http://www.ccndr.org/

German Shepherd Rescue of Northern California:
http://www.savegsd.org/
A friend of mine recently adopted his dog from here

Dogworks Canine Rescue (dobies and greyhounds)
http://www.dogworks.org/
The woman that runs this also volunteers for FOSMAS, and lives about 2 miles from my house!

In terms of finding some of these places, a simple Google search for the type of pet your looking for + state, city name usually yields pretty good results. For example, if someone were to type into Google "german shepherd rescue, bay area", they would likely find several GSD rescue group options.

A great resource about Puppy Mills is: http://www.nopuppymills.com/
This site has been redone a couple of times, but I believe all of the same information is still there. Very good resource.

Adding to the list for "reputable" breeder questions, here are a few more (can you tell I worked in a vet office? *laughs*):
1. what is the difference between "pet quality" and "show quality"?
2. do you require that ALL pet quality pets be spayed/neutered? (this answer should be yes)
3. how many different breeds of dogs do you breed?
(if it's more than one, this could be a red flag. A reputable breeder shouldn't breed more than one...maybe two (if they're very similar like Tervs and Malinois) different breeds of dogs.
4. What steps have you taken to decrease defects in your dogs?
5. What are the good and bad points of the parents, and what titles do they have?
6. Where were these puppies raised? How have you socialized them?
(a good answer will be in the home, underfoot, with other animals, kids, cats...etc.)
7. Do you offer a Health/Hearing/Temperament guarantee with your puppies?
8. Were there any temperament problems in the ancestry of the puppies? Have the sire and the dam been temperament tested?
9. How much time do you spend planning your litters and rearing the pups ?
10. How many litters do you have per year? (this is to see if there is any "overbreeding" going on)
11. Are the sire and dam OFA Certified? BAER tested? Do you have certificates for me to see ?
12. What is the incidence of deafness, allergies, infections, thyroid dysfunction, seizures, stone formation, hip dysplasia, etc., in the pedigree?

Ok...that's all for now.

**hugs**
Karen