While CarMax does allow you to search for hybrids or diesel engines, that's about as green as it gets. You cannot search for flexible fuel engines, for example, or do searches by mileage ratings. Even though the EPA ratings are inaccurate, it's at least a gauge of a car's fuel thirst, and it would be nice to search for this number. CarMax is also limited to a few cities: Los Angeles, Chicago, Baltimore/D.C., Atlanta, Milwaukee, and Orlando.
My recommendation: ignore MyCarMax while you research other sources until you find the car that best suits you. Then, if you live in one of the cities listed above, use MyCarMax once or twice to get a general idea of what's available.
[Source: CarMax, Inc.]