In LabVIEW 2009 one could right-click on a VI, for instance, in the project Files view and select a Delete from Files option. (It didn't work perfectly--in particular, LabVIEW didn't always delete folders from disk, but it usually did work for individual VIs.) NI removed this option in 2010, leaving the developer with the task of deleting files manually through the OS files view. (This isn't the end of the world, of course, if a developer doesn't use integrated version control--and we don't currently but only because LabVIEW does not properly support integration with Subversion--but it is a significant inconvenience.) This option ought to be present once more.
In particular, this function is absolutely required if LabVIEW makes a claim to provide integrated support of version control. On that note, the current client (Pusk Ok SVN) LabVIEW supports for what is probably the most popular version control provider (Subversion) among its customers does not even claim to support file renaming or deletion (http://www.pushok.com/soft_svn.php), while a third party plug-in (http://jkisoft.com/tortoisesvn-tool/docs/) claims to support this behavior only for VIs and Controls (not, for example, LabVIEW class files).