My e-mail organization system was as follows:
1. Delete e-mail that has no long-term relevance or is included in a long chain of replies later on.
2. Do nothing more complicated than shuffle saved e-mail into general folders.
3. When work is slow or you're stuck on an intractable problem or you want to procrastinate, print out the accumulated e-mail, including the ones that say only "I am enclosing x". That's your record that you actually did send x to someone.
4. Delete the files you printed. I tended to save attachments into a separate, public folder so that coworkers could find them if necessary.
5. Pick a binder. A lot of companies use binders with inserts for their reports. If this is the case at your company, scrounge around for some garishly colored insert paper (every office has a stash somewhere) and write "x's e-mails" on the spine insert. Otherwise, pick a binder that's off-color from the usual ones your company uses. Again, you can usually scrounge something.
6. Organize the e-mails in the binder however you want. I tended to use sticky notes as tabs because they were available.
The advantage to having all your e-mails organized is that if you are organized, the chances are good that you will be far more organized than the other people you work with. You and your binder will become a resource. Once people realize that you have this binder, it will get borrowed and disappear all over the office. The horrid or strange binder color is to help you find it again.
So then you go back into the field. When the drill rig is banging away and the reception is all fuzzy, you'll get a frantic call saying "The response to comments is supposed to go out in two hours and we can't find the address of that researcher the EPA wanted us to contact to settle this issue", then you can yell over the din, "Look in my binder. It's probably in section a or b. The binder's retina-searing pink, and if it's not in my office, poke around the offices of x, y, and z."
And you will have saved the day without having the slightest clue what the answer actually was.