clean-buffer-list-kill-never-buffer-names is a variable defined in `midnight.el'.
Its value is
("*scratch*" "*Messages*")

List of buffer names which will never be killed by `clean-buffer-list'.
See also `clean-buffer-list-kill-never-regexps'.
Note that this does override `clean-buffer-list-kill-regexps' and
`clean-buffer-list-kill-buffer-names' so a buffer matching any of these
two lists will NOT be killed if it is also present in this list.

You can customize this variable.