I personally would really use the features of a source control software (you should use one) for this. This would cleanup make independent of your build process. See e.g. svn-cleanup or git clean.
Nevertheless, automake allows some tweaking when to remove which files. This has (intentionally?) built-in limitations on what files generated by autotools can be remove this way though. Have a look at the definitions for MOSTLYCLEANFILES, CLEANFILES, DISTCLEANFILES, and MAINTAINERCLEANFILES and adjust your Makefile.am‘s. With them you can remove a lot of stuff with
make mostlyclean
make clean
make distclean
make maintainer-clean
You won’t be able to remove e.g. Makefile or .deps/ this way.
As for the reliability of make clean it should “work 100%” if you stick to cleanly specifying your files and stay away from manual intervention. Otherwise extend the cleanup rules.