My advice would be to look at TFS no differently than a share out on a file server. Think about each database as a folder. Its subfolders will be tables, stored procedures, views, etc. Then, think about how you would logically organize those folders on your file server. The one caveat is that moving folders around in TFS won't be as easy as moving folders around on a share. So, just get that structure figured out before you start putting things into TFS. DBPro's schema compare should make it relatively easy to pull the structure into a Database Project, and get it into TFS.

So, if your databases are unlikely to change servers, I like:

$\DBA\Servername\DatabaseName or $\DBA\Servername\Department\DatabaseName

And yes, one of the advantages of TFS is having history of who changed what when, so no real value in adding 3rd party databases.