GO Consortium members have recently published several papers on their applications of Gene Ontology terms and annotations in horse, chicken and mouse:

Facilitating functional annotation of chicken microarray data.
Buza TJ, Kumar R, Gresham CR, Burgess SC, McCarthy FM.
BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S2.
PMID: 19811685

Integrating phenotype and gene expression data for predicting gene function.
Malone BM, Perkins AD, Bridges SM.
BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S20.
PMID: 19811686

Structural and functional-annotation of an equine whole genome oligoarray.
Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM.
BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S8.
PMID: 19811692

The Mouse Genome Database: enhancements and updates.
Bult CJ, Kadin JA, Richardson JE, Blake JA, Eppig JT; the Mouse Genome Database Group.
Nucleic Acids Res. 2009 Oct 27. [Epub ahead of print]
PMID: 1986425

You can find these publications, along with many more interesting publications using GO, in the GO Bibliography".