Upgrading a SharePoint farm that are using custom site templates turned out to not be as straightforward as it should. Running Test-SPContentDatabase resulted in several missing web template errors.
The issue is that when you install and deploy custom site templates in your new SharePoint 2010 farm you have to restart your server(s) - an iisreset is NOT enough.
After you have installed your solutions check that the site templates really are available. The template may very well be deployed at \Template\[language]\XML, and even available when you select Create New Site, but that is not enough. Why? Don't ask me.
Run the command Get-SPWebTemplate to actually verify that the template is really there.
I struggled hard until I found this article: http://projectserverblogs.com/?p=4294
After removing, reinstalling, redeploying and rebooting and running the powershell Test-SPContentDatabase one more time, all the Site Template releated errors where gone!