Chris,
I am in charge of overseeing users that manage roughly 6,000 dwg files in PDMWorks. Could you be more specific? For us, PDMWorks does all that we need it to as far as handling DWG files. The bulk import in the admin tool worked wonders for getting all 6000 of our files out of another data managment vault and into PDMWorks. Joy Pineau contacted us during the development of the bulk load tool and we gave our comments on an alpha version. We were very pleased in how well it migrated our files over. We were able set up attribute maps so that all the information in our DWG title blocks were read and written to file properties in PDMWorks. All of our DWG files are now searchable within PDMWorks. As far as XREFs, our files contain XREFS to basic elements of the drawing format that are outside the vault. There are no issues with XREFs for us, but we may be using them totally different than your company may be. If you could be more specific I could maybe give some answers and run a few tests. eDrawings (the built in viewer in the vault) does a pretty good job at viewing the DWG files as well. There is a setting under tools, options, for it to search known locations for XREFs so that they too are viewed in the DWG file.
Pete