Gmail Apps (not sure if this is available in Gmail) has a feature called Tasks. Tasks is part of the email system. Like Outlook and Apple Mail, it gives you a place to list TO-DOs. You can start as many Task lists as you want so you can keep things in categories, or, perhaps, organized by project.
What makes Tasks unique from anything I have used before is the ability to connect an email conversation to a Task and rely on its listing there as both a reminder that follow up is needed as well as provide the background reference itself. Simply clicking on "related email" brings up the original email along with all others in the thread/conversation no matter how old or where you may have filed them.
Another advantage is that you can rely on Tasks to track critical emails and not clutter up your inbox with special "stars" or colored "flags".