I have tried to debug PHP code in Aptana 3.0.4, however without success.
P.S.: I am using Symfony 1.4 and I want to debug the PHP code.
It's not possible yet on a plain vanilla version of Aptana Studio 3, but it will be possible soon (I hope).
If you want to debug PHP, and only have the Aptana's editors support, you will need to install PDT on top of it and use its debugger capabilities for now. However, keep in mind that you will have two different plug-ins that will support PHP, so you have to make sure that the projects you create support one or the other. That is, if you would like to use Aptana, create a project using the Aptana PHP project wizard, and if you want to use the PDT editors - create the project using the PDT project wizard. That will prevent a major 'indexing' and 'code assist' headache.
As for the breakpoints - Those will probably need to be set on the PDT PHP editors (you can define the editor that takes over the PHP extensions through the preferences - Content Types and 'File Associations'). Otherwise, the PDT might ignore those when starting to debug.
I know that's a little messy right now, but it will get better.
Hope that helps.
[UPDATE 6/25/2012]
Aptana Studio now supports PHP debugging. Right now it's on the nightly stream (3.3.0), and you can grab it by updating the Studio for the latest. Installation instructions are at http://preview.appcelerator.com/studio (Studio Tab), and it should be available tonight (6/26/2012).