How to make a city more ecological is already made in a lot of places. Here is a list of places I've visit lately and some more of what an ecological city might be.

Trip through Europe;
Green roofs and green cities
Make'n a good feeling in the city?
Eco-town Amersfoort
Green walls
Animals in the city
Urban agriculture
Streets in greenery
Greening the streets
Garbage solutions
These cars and carfree cities
Interaction human-street
Bike lines and bike roads
Through Europe with one ticket

Pictures from South Germany
Französisches Viertel, Tübingen, Germany
Example from Tübingen
Vauban, Freiburg, Germany
Freiburg, The Green City
Le Halles, in Paris
Göteborg and Älvstranden in Göteborg
Green spots in Istanbul
Cars and ugly spots in San Francisco Bay Area
The city forest in Alingsås
The "ecopath" in Hjo
Hammarby Sjöstad in Stockholm
The Western Harbour in Malmö
Houses and green spots in Copenhagen
Terrace house and green spots in Warsaw
Green spots in San Francisco
Slope houses in the hill of Berkeley
The old bewery house in Skövde
Ecoarchitechture house in Uppsala
Why so ugly?
Public transit over the world

About ecocities
What is an ecocity? part 2
What is an ecocity?
Face of an ecocity
A city perspective in your own imagination
Living in the future with some examples

The Boverian house  (winter-garden greenhouse with apartments connected)
New York with car free plaza
15 examples of green cities
Vancouver EcoDensity Initiative
Plans for sustainable cities and ecocities
Ecoplans for Treasure Island, San Francisco