Just one tiny bit that almost hijacked my friday evening I want to share with possible other victims of suPHP 
Any 3rd party extension in the backend of a TYPO3, I just wanted to tweak, would fail to run, i.e. phpmyadmin. It results in an internal server error and the http status code 500. So what to do?
After getting access to the error.logs it came clear. Make sure you have checked the filesystem for writing access. On this machine there is suPHP and in the end it just complained about the directory typo3conf/ and it’s child folder ext/ which were both writable by it’s owning group.
# chmod o-w typo3conf # chmod o-w typo3conf/ext
Lucky me, now the extensions work just fine.
Premature end of script headers: index.php, referer: http:// helloworld /typo3/alt_main.php
You may have something like this in your error.log too. Have a look at the suPHP faq for this.
Why do my scripts not work and why do I get an “Premature end of script headers” in the error_log?
You probably have installed the CLI version of PHP, but you need the CGI version. Copy the file /build/path/sapi/cgi/php to /where/ever/you/have/installed/bin/php to use the CGI version.