Refineries can be used to increase the efficiency of your extractors.  Increasing the loyalty of your planets (via culture, for instance) will also increase extractor income.

You can also take neutral extractors--the metal and crystal asteroids in gravity wells where you cannot colonize anything (asteroid belts, ion storms, gas giant planets).  If you are Vasari, you use your scouts, which is one of Vasari's big advantages.  If you are Advent or TEC then you need colony frigates (mothership capital ships cannot do it).

Well you could build trade ports, and get credits and then buy or sell for more.