A current benchmark set based on HOMSTRAD multiple alignments and SABMark twilight zone alignments is available Here (479MB download). Alignments (FASTA and PDB files) are provided for each sequence aligner Formatt can use. If you use Formatt, please cite both: "Noah Daniels, Shilpa Nadimpalli, and Lenore Cowen, "Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment," BMC Bioinformatics, in press.
AND "Matt Menke, Bonnie Berger, and Lenore Cowen, ""Matt: Local Flexibility Aids Protein Multiple Structure Alignment," PLoS Computational Biology, Vol. 4, No 1, 2008.
Benchmark alignments produced by Formatt 0.97 (Shilpa Nadimpalli, Noah Daniels and Lenore Cowen, "Formatt: Correcting Protein Multiple Structural Alignments by Sequence Peeking," in Proceedings of the 2011 ACM Conference on Bioinformatics, Computational Biology, and Biomedicine.) are available for download here.