My work email has a size limit on my mailbox so I don't keep all my reference in my mailbox that's stored on the company's servers. Instead I create a local PST file and add it to outlook. The PST file is stored locally on my hard drive so I can move whatever I want there without a network storage quota to worry about.
I try to keep it as linear and simple as possible. I've taken the advice that David Allen talks about in his book regarding reference. Instead of creating a deep hierarchy of reference folders, I basically have a simple list of alphabetical topics that come to mind. In his second book, David remarks that organizing your reference folders is a self-policing activity that you need to experiment with over time. It's an organic process that is unique to each person. The goal that I think should be strived for is the ability to quickly access the information you want without being bogged down in the organization. If the organizational format prevents your from being organized, then your organizational format isn't very organized.
Recall that David suggests making lots of folders in your paper based reference system, giving them a subject name that accurately describes the content. I'm currently experimenting with maintaining 3 reference systems at work - paper based in a filing cabinet, electronic based as folders on my desktop, and email based as folders in my local PST outlook file. I use the same theme in all three and it's working pretty good so far. As a software engineer, I've been able to quickly (within 2 minutes) find exact, particular material/conversation that I've worked on months ago. In my line of work, that's quite rare indeed. That's probably been one of the biggest boons to my career so far with implementing GTD.