The GO Consortium has an update in the 2010 NAR Database Issue:

The Gene Ontology in 2010: extensions and refinements.
The Gene Ontology Consortium.
Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. Epub 2009 Nov 17.
PMID: 19920128

The 2010 NAR Database Issue also includes articles on numerous databases that use GO in various ways.

GO Consortium members have also published a paper on using GO to study developmental biology:

Representing ontogeny through ontology: A developmental biologist's guide to the gene ontology.
Hill DP, Berardini TZ, Howe DG, Van Auken KM.
Mol Reprod Dev. 2009 Nov 17. [Epub ahead of print]
PMID: 19921742

From outside the GO Consortium, two recent papers describe the use of GO to study human evolution:

Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs.
López Herráez D, Bauchet M, Tang K, Theunert C, Pugach I, Li J, Nandineni MR, Gross A, Scholz M, Stoneking M.
PLoS One. 2009 Nov 18;4(11):e7888.
PMID: 19924308

Phylogenomic analyses reveal convergent patterns of adaptive evolution in elephant and human ancestries.
Goodman M, Sterner KN, Islam M, Uddin M, Sherwood CC, Hof PR, Hou ZC, Lipovich L, Jia H, Grossman LI, Wildman DE.
Proc Natl Acad Sci U S A. 2009 Nov 19. [Epub ahead of print]
PMID: 19926857

These and many other new publications are now available in the GO Bibliography".