Seeking open vector format for long term GIS data storage in off-line repositories?

In my opinion, Shapefile is a good choice, but it has many limitations for historical reasons. For example, a single shapefile cannot be greater than 2GB, etc. You have to decide whether to commit to those restrictions if you use shapefile as the archival format. There is a good discussion at GIS.SE as to Are there any attempts to replace the shapefile?.

For archival purposes, a good choice may be to use text formats, such as GML, GeoJSON mentioned in the above post, or even Well Known Text (WKT). Text formats are most portable, readable forever, and (so far) without license issues. We can always reconstruct auxiliary files 50 years later from the basic data. To separate concerns, one can choose an efficient/reliable method/format to compress the text files before archiving them.

The shapefile could be considered an open format in that its technical description is published and routines for reading and writing the format can be created without requesting permission or paying license fees.