Here are safe from Monsanto seed companies.

Abundant Life Seeds (Cottage Grove, OR)

Amishland Seeds
Annapolis Valley Heritage Seed Company canada
Baker Creek Seed Co. (Mansfield, MO)
Berlin Seeds - they don't have a website. Atleast I didn't find one.
Botanical Interests (Broomfield, CO)
Bountiful Gardens (Willis, CA)
Diane's Flower Seeds (she has veggies now, too)
Fedco Seed Co. - phasing out seminis seeds. (Waterville, ME)
Garden City Seeds

Good Seed Company (Oroville WA) - cold hardy, short-growing season plant seeds

Heirloom Acres Seeds -I've heard from several people thier seed germination is poor and so is thier customer service.
Heirlooms Evermore Seeds
Heirloom Seeds (West Elizabeth, PA)
High Mowing Seeds
Horizon Herbs
Irish-Eyes (Ellensburg, WA)
J.L. Hudson, Seedsman (La Honda, CA)

Kitchen Garden Seeds
Lake Valley Seeds
Livingston Seeds
Local Harvest
Mountain Rose Herbs
Native Seeds/SEARCH - Tuscon, AZ (specializes in southwestern and northern Mexico-adapted seed)

Natural Gardening Company (Petaluma, CA)
New Hope Seed Company
Nichols Garden Nursery (Albany, OR) (According to January 2012 email asking about Seminis seeds, Rose Marie Nichols McGee said Nichols stopped selling Seminis seeds more than two years ago. Info from NWRaven)

Organica Seed
Peaceful Valley Farm Supply
Renee's Garden (Felton, CA)
Richters Herbs

Salt Spring Seeds (Salt Spring Island, BC, Canada) US Customs does not allow shipping seeds to U.S.

Sand Hill Preservation Center
Seed Saver's Exchange (Decorah, IA)
Seeds of Change (Santa Fe, NM)
Southern Exposure (Mineral, VA)
Sow True
St. Clare Heirloom Seeds
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) - (Cottage Grove, OR)
Tiny Seeds
Tomato Fest - ask for bubble pack when ordering from them for seed viability
Trees of Antiquity
Underwood Garden Seeds
Uprising Seeds
Victory Seeds (Molalla, OR)
Wild Garden Seed - (Philomath, OR)

Wildseed Farms
Wood Prairie Farm