For new green building products, the main supplier in the Portland area is Ecohaus, which was formerly known as the Environmental Home Center. They offer a good selection of FSC Certified flooring and decking, low VOC paints, sealers and adhesives, cork and marmoleum flooring, earth plasters, low flush toilets, energy saving lights, and water conserving plumbing fixtures.
Another important local resource is the ReStore which is run for the benefit of Habitat for Humanity and offers the largest inventory of used building supplies. Some of their products include windows, interior doors, bathtubs, toilets, sinks, appliances, lighting/electrical hardware, cabinets, flooring, drywall, tile, and assorted hardware, etc. They also offer a full service demolition crew which can help with material recovery.
If you are just looking for flooring options, then you can try Eco Floors on Milwaukie Ave. They carry low VOC carpet, recycled carpet, Bamboo floors, and FSC certified wood floors.
For lumber, several of the local lumber yards carry FSC Certified lumber in stock and most can special order it.