Hundreds of organizations are working to build sustainable local food systems and educate people about the issues involved in modern food production. Here's a sampling of some of the best websites:
Center for Food Safety,  a non-profit public interest and environmental advocacy organization established for the purpose of challenging harmful food production technologies and promoting sustainable alternatives.
Cornucopia Institute -- A watchdog/research group for the organic movement.
Environmentally Concerned Citizens Organization of Gratiot County (ECCO) -- A grassroots organization in Michigan inspired by the infiltration of factory farms in the region.
Environmentally Concerned Citizens of South Central Michigan (ECCSCM) -- A gangbuster watchdog group keeping tabs on the relentless factory farm pollution in this part of the state.
FACT -- Food Animal Concerns Trust, a Chicago-based group dedicated to improving the lives of farm animals
Farm Aid -- The group founded by Willie Nelson and John Mellancamp to help farmers in the 1980s began with a concert more than 20 years ago and has since become a powerful resource for both farmers and consumers interested in supporting sustainable agriculture.
Farm Sanctuary-- a farm animal protection organization with shelters in New York and California that are well worth visiting.

Food and Farm Watch -- This organization has created a map of the locations of all factory farms in the United States and compiled stats of the states and counties with the most CAFOs. Extremely valuable info.  Check it out!
Food Routes -- All about why buying from local farmers is the way to go.

ExtraVEGANza -- A Calvin College prof's extremely fun and informational vegan recipe website.
Grassroots Action Center for the Environment (GRACE) -- An excellent organization that provides a wealth of information about sustainable and factory farming. 
Growing Power -- Very cool Milwaukee-based organization that provides hands-on training, on-the-ground demonstration, outreach and technical assistance for the development of community food systems that help people grow, process, market and distribute food in a sustainable manner.
Heifer International -- This organization seeks to end hunger worldwide by promoting sustainable agriculture.
Humane Farming Association-- Just what its name implies...
Humane Society of the United States -- In recent years this venerable organization has tackled the topic of factory farms with inspiring commitment and vigor.
Organic Consumers Association -- Their motto is "campaigning for health, justice and sustainability."

Metrofarm -- An online magazine for "metropolitan agriculture."

New Farm -- A very informational website for farmers and consumers created by the Rodale Institute.
People for the Ethical Treatment of Animals -- This well-known animal activist group is one of the leaders in the battle against the inhumane treatment of farm animals.

Sierra Club Mackinac Chapter -- The Michigan chapter of this national group has been on the frontlines of fighting CAFOs on environmental grounds for several years now.  Support them!
Sustain -- Seeks to create a sustainable world through projects like familyfarmed.org.
Sustainable Table -- Everything you ever wanted to know about factory farms but were afraid to ask is provided by this website of the Grassroots Action Center for the Environment (GRACE)