I think you want to do it in the search.php, anyway. This is for "Todays Active Threads".
Find:
PHP Code:
$wheresql.=" AND thread.open<>10";
and replace it as:
PHP Code:
$wheresql.=" AND thread.open<>10 AND thread.forumid!=X";
If you want to do more than one forum, change it to this:
PHP Code:
$wheresql.=" AND thread.open<>10 AND thread.forumid!=X AND thread.forumid!=X";
There are 2 instances, one is for members, the other is for guests. If you want to exclude forums for both of them, change both lines.