Apparently CDC means "Connected Device Configuration", and is intended for mobile devices. See this link for more information:
http://developers.sun.com/mobility/configurations/articles/cdc/.
So it seems like unless you're developing for a mobile platform, you just need the normal non-CDC JARs. To develop for a mobile platform, you need to use OpenGL ES1 or ES2 and the CDC JARs. See here for details:
http://jogamp.org/wiki/index.php/Jogl_FAQ#How_to_develop_Cross-Device_Applications.