`rm` is definitely one of them, it's just suppressed by the `-f` flag. (examples from Ubuntu)

    $ touch foo
    $ chmod -w foo
    $ rm foo
    rm: remove write-protected regular empty file ‘foo’?

There's also the immutable attribute many modern filesystems support, which prevents the file from being modified unless the attribute is removed.

    $ sudo chattr +i foo
    $ rm foo
    rm: remove write-protected regular empty file ‘foo’? y
    rm: cannot remove ‘foo’: Operation not permitted