So this is strictly Drupal, but it's a useful post which will hopefully help others who may have this problem.
I use PHPStore or Aptana Studio 3 for developing in Drupal. Aptana is a great IDE in my opinion. Occasionally it gets into a mess and hangs every time I launch it and Windows reports and Aptana Studio 3 is not responding - very annoying.
The simple fix is to remove the .markers file from the project which could be causing the issue. This file (as far as I know) contains break points, so you'd need to re-add them to your project.
The location of the .markers file is \Aptana Studio 3 Workspace\.metadata\.plugins\org.eclipse.core.resources\.projects\<Project Name>.
That's all - it should be good now.