Im trying to configure xdebug to work with Netbeans 6.9 and php 5.3 As far as i concern i have setup xdebug properly. I can see xdebug extension from phpinfo page.
An alternative is the Dephpugger project. Is like ipdb in python or byebug in Ruby. https://github.com/tacnoman/dephpugger
Is very easy to use.