Tregwiki:Gene Ontology Tools
There are probably hundreds of GO tools. I don't know many. Have a look at the Genontology Website for a better overview.
gostattoolbox most accessed article of genome biology, used by a recent paper
NCBI Entrez Genes GO data in an easy tab-delimited format for simple loading into script-languages (mentioned by alexander morgan on the biopython list)
there is a similar thing for plants somewhere on tigr.org.
Wego: Upload your gene lists and see which category or sub-category is over-represented. The page has a good linklist for GO and graphics-tools.
Gostat: Seems to be the same thing as Wego...?
ease Genebank to overrepresented category tool
[GObar] Sort Gene lists by Gene Ontology anntations
[The Ontologizer can apprently better cope with the complex parent-child distributions of GO
[FUNC] claims to be better in its statistical approach than Gostat, is a lot more recent and, est of all, available as a standalone PERL-Program. In addition, it's author is very helpful.