chmod -r uses symbolic mode. Specifically it removes read permissions for the file. Other forms include w for write and x for executable. + can be used to add permission.
ls -r actually lists entries in reverse order! It needs -R as well.
cp and rm accept either.
Looking at some man pages the only commands I found where -R didn't work were scp and gzip where it doesn't do anything, and rsync where it's "use relative path names".
(Caveat: BSD utils might be different, who knows what those devils get up to!)