I'm currently working on some Symfony2 bundles and I have one Netbeans project for the main Symfony2 app and one project for the bundle. [...] The debugger starts for the "main" project, which is the Symfony2 app, but setting breakpoints with Netbeans (y'know, by clicking the line number) for the bundle doesn't really work, as those are in the other project and not in the debugged one, rendering the whole debugging useless.

The fix is pretty simple, if a bit manual - simply place xdebug_break calls in your code anywhere to tell the debugger to stop there. It's not as friendly and automatic as just clicking in the IDE, but it gets the job done. For more information on Xdebug, see their site.