cPanel sucks.. Poorly coded, worded, packaged. Almost-decent documentation, but looks messy and unprofessional. Plesk is much better!
phpWiki won’t run properly when installed from cPanel.
It will print out this error message:
lib/Request.php:299: Warning: ob_start(): output handler ‘ob_gzhandler’ cannot be used after ‘URL-Rewriter’ or something

This can be fixed by uncommenting 1 line in index.php:
define(‘COMPRESS_OUTPUT’, false);

UPDATE: Not sure if this is still valid, since I found this issue in March 2005.