The NRDC has a site which provides guidance on a Building Green: From Principle to Practice. It does a nice job of summarizing the process, and it is supplied by an experienced Architecture firms.
Even though this site wasn't intended for data centers, it provides good guidance on the stages of a Green Data Center project which many companies follow, but haven't taken the time on how to explain what they are doing.
Good leadership is important to the success of any building project, but it is particularly vital in green building efforts. Some members of your building and design team may not be accustomed to thinking about a building as a single, well-integrated system -- a key strategy in green construction -- so make sure everyone you're working with is committed to thinking ahead and working collaboratively.
The best green strategies achieve multiple objectives with a single solution. The earlier you decide to build green, the more opportunities you'll have to maximize the synergies in your building's design and performance.