Here are some common logs files that you should clear periodically.

apache access_log / apache error_log / suexec_log / suphp_log(if you use suphp as PHP handler) under
/usr/local/apache/logs

exim_mainlog / maillog / exim_paniclog /exim_rejectlog under
/var/log

Cpanel access_log / error_log / login_log / stats_log / chkservd under
/usr/local/cpanel/logs

You can clear logs either using ConfigServer Explorer via WHM or using “>” in SSH (ex. root@user [~]#> error_log).