Some other good ones in the Philly area:

Ardmore Music Hall
http://www.ardmoremusic.com/

World Cafe Live
http://www.worldcafelive.com/

Union Transfer
http://www.utphilly.com/

The Trocadero (over 1000, I believe, but the smaller Balcony section holds 2-300)
http://www.thetroc.com/

Kennett Flash (capacity's only around 100, but the director's a devoted proghead and there are pretty regular patrons)
http://www.kennettflash.org/

And a few in northeast PA

http://www.scrantonculturalcenter.org/
http://www.kirbycenter.org/
http://www.theleonardtheater.com/
http://www.riverstreetjazzcafe.com/