What are the best features to integrate when building a new "green" home?

I’m planning on having solar panels and using rain/graywater for the toilets, but as I’m building custom from the ground up, are there other features I should be talking to my architect about?

I would suggest focussing first on optimizing the energy and water use/efficiency, improving the Indoor Air/Environmental quality, and optimize the design for resource conservation rather than going directly into renewable energy approaches. Solar panels should be one of the last items on your list since a significant part of the energy savings can come from a good Green Building design.

Here there are some areas you can target:
-Climatic design (windows locations, natural shade, overhangs, thermal mass to absorb and emit heat when needed). The idea is to get as much passive heating and cooling as possible each day.
-Foundations: Radon mitigation, use fly-ash for concrete, insulation, sealed crawl spaces.
-Framing: use OVE Optimal Value Engineering, engineered lumber, trusses, use FSC certified wood.
-Roofing: cool roofs, radiant barriers
-Windows: Low-E, lower u-factor and Solar Heat Gain Coefficient. Good installation practices to avoid air leaks.
-Insulation and air infiltration: mainly quality installation, recycled materials. Airtight building envelope, good design mechanical ventilation, and makeup air to avoid air leakage going into or outside of the house.
-HVAC: use a designer to get the load, ducts, and registers selections correctly. Not oversized equipment and ducts.
-Furnace and water heater: energy start, Water Sense certified. High efficiency and proper design. Water heating distribution systems (pipes) are as critical as high-efficiency equipment. Heat recovery systems, recirculation pumps, solar water heater, grey water recovery as you mentioned.
-Finishes: low VOC, low formaldehyde, renewable, resistant.
-Electrical: energy start and high efficiency fixtures. Solar panels
-more…

Please don’t feel overwhelmed by all these options; a Certified Green Building consultant can help you to narrow down and prioritize which are more relevant in your case. Again, as I said, renewable energy is great, but you can achieve so much more by making the right design decisions.

Wow, this is a great, comprehensive list!

How much of this needs to be communicated to/coordinated with the architect vs the builder? Climatic design and roofing seem to clearly need architect input, but who do you communicate with around the foundation, insulation, framing, etc.? Or will a Certified Green Building consultant act kind of like an Owner’s Rep and communicate directly with your architect/builder/electrician/HVAC specialist?

Architects usually get the Green Building sheets filled before getting the construction permit. They use a Green Building Consultants to prepare the forms. But I believe going with a Green Builder can give you more input in the design phase as he can also assess cost vs. benefit.
Most of the design features are selected before the builder comes into play, but a good practice is to use involve the Builders in the design review meetings with the architect to provide timely feedback.
After the design is finalized, it needs someone focused on quality installation to make those systems work. Sometimes good design practices are already specified in plans and construction specifications, but a poor installation can prevent you from getting the benefits or even create a new problem for your home.
I’m happy to help if the project is in the SF Bay Area.