Baselayer keep you warm and dry, moving moisture away from your body. A good baselayer also keeps the seams away from your body for comfort. I've always considered Patagonia the standard for green base layers to stay warm. They are made from 64% recycled polyester and are recyclable through the Common Threads Recycling Program.
For your body, another great find from Patagonia is their simple waterproof/breathable Eco Rain Shell. This 2-layer shell made of 100% recycled polyester and also Recyclable through the Common Threads Recycling Program.
For your feet, Timberland's Waterproof Torrance Oxford will help you maintain your business casual while avoiding swampy toes all day. Timberland is known for it's environmental stewardship and uses recycled boxes on all their shoes, aims to become carbon neutral by 2010 and designs many of their products to be recyclable.
For your stuff: I purchased my Timbuk2 before they were available in Hemp (67% natural Hemp fibers and 33% PET from recycled plastic bottles) but unfortunately the hemp ones are not waterproof. If you need to keep your stuff dry, the standard Timbuk2, in ballistic nylon, has a waterproof liner. Though they're not made from recycled materials, their custom bags and classic messenger bags are made locally in San Francisco. Those that are not are made by workers whom they ensure receive good wages and have working environments, enforced by Timbuk2 by regular factory visits every 4- to 8 weeks.
On your Bike:
SykesWoodFenders makers beautiful wooden fenders for your bike from wood, including tight vertical grained Douglas Fir from reclaimed mill ends.
Safety with Lights:
Cateye's new Single Shot not only uses LED lights but is rechargeable. Lasting up to 3 hours on high beam or 36 hours on flashing. It has a direct charging port so just plug it in once a week and you'll be set.
You've probably seen the Cycloc on various green blogs (including AT) but it is for sale. Made of 100% recycled MDPE plastic it is an elegant storage solution for apartments and garages alike.