Official mirrors
Medical College of Wisconsin Milwaukee, WI
Duke University Durham, NC
Cornell University Ithaca, NY
Department of Molecular Medicine (MOMA) at Aarhus University, Denmark
Queensland Facility for Advanced Bioinformatics (QFAB) Australia
Others
EyeBrowse National Eye Institute, NIH - Eye-related genes and RNAs
dbRIP - Retroposon Insertions Roswell Park Cancer Institute, MD
Arabidopsis thaliana at UCLA (near complete mirror)
Schizosaccharomyces pombe (fission yeast) at NCI, NIH
Plasmodium falciparum (malaria parasite) at Ares Lab, UCSC
Human non-coding - China
U of Chicago - full mirror
U of Copenhagen - full mirror (not quite fully sync'd).
U of Washington - hg17 mirror with structural variation data (Eichler lab).
CNIC, CAS - Computer Network Information Center, Chinese Academy of Sciences -- partial mirror, not fully current (v197 vs v204 on 04-22-2009.)
NCI - The Cancer Genome Atlas (TCGA) at the National Cancer Institute.
Solanaceae - Some small sequences from tomato, potato, petunia, pepper and eggplant. - Cornell.
Human, Mouse, Rat, D. melanogaster, B. mori, C. elegans - ncRNA.org
WUStL - full mirror plus Epigenomic Roadmap data, Washington U, St. Louis