We recently had a client we assisted with migrating from MOSS to SharePoint Server 2010. This migration posed a challenge due to the fact that this client had several sites that were built from the Fab 40 Templates (Application Templates for Windows SharePoint Services 3.0). After doing further discovery work with this client, it was determined that only one of the sites was truly being used; however, since this was a detach DB migration plan we decided to not remove those sites until after migration. This allowed us to keep the current farm in place in case we needed to roll back after migration. For what it’s worth, we now believe this to be a mistake. If at all possible, make sure you remediate any sites and features in MOSS before doing a migration.
If, on the other hand, you do end up deleting Fab 40 Sites after migration, you may end up with the dreaded “Missing Server Side Dependencies” error message in your Health Analyzer.
After much research we determined that the issue was not a orphaned feature, but simply that the original site was still in the content database because it was still in the Recycle Bin. Simply removing the site from the Recycle Bin cleared up this Health Analyzer rule in this case. SharePoint will probably clear this up for you in about 30 days after migration when it cleans out the Recycle Bin, but if you would like to resolve this error message without waiting you can do so by deleting the deleted sites from your Recycle Bin manually. Just be sure you truly never want to restore those sites. Hope this helps.