The Gene ontology web site provides annotation files for a variety of species which can all be downloaded and imported into the CLC Genomics Workbench. They can be used to annotate experiments as shown in Adding annotations. They can also be used with the Gene Set Test and Create Expression Browser tools.
Import GO annotation file using the Standard Import tool. For GO annotation files in GAF format, use the option "Force import as type: Gene Ontology Annotation file" from the drop down menu at the bottom of the Standard Import dialog.
See the list of available files at http://current.geneontology.org/products/pages/downloads.html.