We have developed a pipeline to predict genes based on homology using Guy Slater's exonerate and predicted genes in various species. Gene predictions are available for browsing and download.
Flies Gene predictions in Drosophila species as part of the AAA Project. Also available for download are multiple alignments, orthologogy assignments used in

Heger & Ponting (in press) Evolutionary rate analyses of orthologues and paralogues from twelve Drosophila genomes.

Mammals Gene predictions in Opossum (Monodelphis domestica) and Platypus (Ornithorhynchus anatinus).