Last I checked, there was an eclipse CVS bug (https://bugs.eclipse.org/bugs/show_bug.cgi?id=79869) that made it impossible to use CVS with Worklight projects.
The Worklight Infocenter has information on what/what not to check in: http://pic.dhe.ibm.com/infocenter/wrklight/v6r0m0/topic/com.ibm.worklight.help.doc/devref/r_integrating_with_source_contro.html
I've used Rational Team Concert, Subversion and Git with worklight projects, all with success.
I have a (somewhat dated) blog post on using Subversion with Worklight here: https://www.ibm.com/developerworks/community/blogs/dhuyvett/entry/using_source_code_management_with_worklight_subversion?lang=en