Not sure if this is the best forum for this. Is there any software that makes large projects easy to develop? Like create a flow-chart in which things need to be finished, a place for notes and or a list of things needing to be done?

The reason I ask is I want to create a program with PHP and MySQL and it would be a lot easier to create it with something I already made that outlined what functions I need and where and what they do and the features each page should have.

Most project management software I've seen are either geared for or created with Java (shudder) or are completely unrelated for software/web development. So what are the top ones for development?