I found a tutorial explaining what I wanted to do:
http://download.oracle.com/otn_hosted_doc/sqldev/Glossaries/glossaries_viewlet_swf.html
on the download page under demonstrations "Working with Glossaries"
This was for version 3 (of the Data Modeler, which is part of the sql developer). In version 4, the "Preferences" window shown can be opened by right clicking on the top node in the Data Modeler > Browser view and going to properties (settings?).
This is also worth reading:
http://www.oracle.com/technetwork/developer-tools/datamodeler/datamodelernamingstandards-167685.pdf