Here are safe from Monsanto seed companies. Please reply with what I have missed and I will add them to this list.
Abundant Life Seeds
Annapolis Valley Heritage Seed Company canada
Baker Creek Seed Co.
Berlin Seeds - they don't have a website. Atleast I didn't find one.
Diane's Flower Seeds (she has veggies now, too)
Fedco Seed Co. - phasing out seminis seeds.
Fisher's Seeds - 406-388-6052 They don't have a website, but they will send you a catalog if you give them your address
PO Box 236, Belgrade, MT 59714
Heirloom Acres Seeds -I've heard from several people thier seed germination is poor and so is thier customer service.
Heirlooms Evermore Seeds
High Mowing Seeds
Kitchen Garden Seeds
Lake Valley Seeds
Mountain Rose Herbs
Native Seeds for the Arid Southwest
Natural Gardening Company
New Hope Seed Company
Peaceful Valley Farm Supply
Sand Hill Preservation Center
Seed Saver's Exchange
Seeds of Change
Territorial Seed Company *Tom Johns, the pres. of Territorial posted in the comments on my blog about Seminis being owned by Monsanto, and said customer service will provide a list of seeds they buy from Seminis, so you can avoid them. He also said that Seminis is providing less varieties every year (typical of Monsanto) and they are finding suitable replacements. So, don't count them out completely.* (info from AdinaL)
Tomato Fest - ask for bubble pack when ordering from them for seed viability
Trees of Antiquity
Underwood Garden Seeds
Wood Prairie Farm