Supervisory controllers, and methods, for use in a coordinated IAQ and economizer system. Various control objectives are defined and met. Some illustrative control objectives include economizer control, sequencing of economizer free cooling with compressor driven cooling, indoor air quality and FAV aims, demand ventilation settings, system protection from low temperatures, and smoke, supervisory and fault tolerance commands. The controller may be self configuring. A tiered fault tolerant controller is also provided. An illustrative controller is configured to determine whether various system sensors and devices are operational. The illustrative controller is also configured to perform a first method when all system sensors and/or devices are functioning, and at least a second method in response to sensor or device failures. The supervisory controller may include integrated economizer control, or may be configured as a separate controller. Supervisory controllers configured for use with specialized controllers are also illustrated.