Berkeley Drosophila Genome Project
Drosophila Heterochromatin Genome Project
Homophila (thanks to Max Casu for drawing this to my attention) - compares human and fly genomes. Care with spelling if typing in the URL!
Interactive Fly - this has an A-Z index of genes
NCBI Entrez , perhaps in particular: Gene; Nucleotide; SNP; Taxonomy. Gene searches Flybase (see above) and provides links to PubMed
NCBI Map Viewer, graphical view of the D. melanogaster genome
WWW Virtual Library: Drosophila