Today CLIR published a report which is designed to provide guidance on the acquisition of archives in a digital world. The report provides recommendations for donors and dealers, and for repository staff, based on the experiences of archivists and curators at ten repositories in the UK and US, including the Bodleian. You can read it here: http://www.clir.org/pubs/reports/pub159
The Library of Congress has released some open source tools for transferring archives at (see Library of Congress Transfer Tools at Sourceforge). The tools support the Bagit specification, and can check for missing, extra and duplicate files as part of the process. Transfers can be made using rsync, http and ftp. The verify script also checks hash values of files against those listed in the Bagit manifest.