I just installed BDI/EMC Debian kernel Linux on my Sherline mill - I can run g-code written with a text editor just fine. But all of the CAD programs on the disc (Sherline) save in a format that EMC will not load (Synergy and QCAD). Is there a good Linux based CAD program that will generate g-code in a format that I can read? Preferably Linux GNU based. Or is there a conversion program for .syn and .dxf files?

check this link:
http://www.ribbonsoft.com/camexpert.html
emc does not understand dxf files, the above will convert your dxf to an nc file, upload that to emc.
jerry