Two great papers:

Use and misuse of the gene ontology annotations. Rhee et al., (also pointed out by Pierre); http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg2363.html

And an overview of 14 tools performing GO enrichment analysis

Ontological analysis of gene expression data: current tools, limitations, and open problems. http://bioinformatics.oxfordjournals.org/cgi/content/full/21/18/3587

Klaas

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Klaas Vandepoele, PhD
Tel. 32 (0)9 33 13822
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, Belgium
E-mail: Klaas.Vandepoele@psb.ugent.be
Website: http://bioinformatics.psb.ugent.be/
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Not shy of a spark, a knife twists at the thought 
that I should fall short of the mark