PLEASE DON'T ANSWER TO MY POST, as it's a post from 2007
I was wondering the same for NWDS 7.31
-clean doesn't do the job (it simply does a file synchronization between Eclipse/File system at startup)
The solution is:
-data "C:\path to the default LOCAL workspace you want"
you may enter this line in the SapNetweaverDeveloperStudio.ini file
Reference: Setting Workspace Using the -data Parameter - SAP NetWeaver Composition Environment - SAP Library