The problem is that if the path to PEAR is incorrect in the filter settings any node that uses it will display a blank page. No error message, just blank. Which means that PHP is killed somehow. I haven't found the real reason for this (and it's a mystery for me how a modern web environment such as PHP is so vunerable).

The real problem, however, is that if you have at least 1 node with a PEAR Wiki Filter enabled input format and search module enabled, this will effectively stop cron.php from running on your site at all (it invokes and index update that renders new nodes).