When using CVS I always use cvspurge (from the CVS Utilities package) to delete the auto generated files that are not deleted by make distclean, this is useful to test local and uncommitted changes in the otherwise clean source tree.

This is why some months ago I wrote a purge extension for Mercurial. Now my code, improved by Emanuele, has been included among the official extensions so it will be shipped in the Mercurial packages of all distros.