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version control is a huge issue, metadata should play a big role.
I think the stock/obvious answer would be to use a spatial database (PostGIS, Oracle, SDE, MSSQL Spatial, etc) in conjunction with a metadata server such as esri's GeoPortal or the open source GeoNetwork application, and overall I think this is generally the best solution. However, you'll likely always have a need for project-based snapshots / branches / tags. Some of the more advanced databases have ways of managing these, but they're generally not all that easy to user/manage.