I have a folders for each campaign (one which I run, two in which I play).]
The ones in which I play have folders like "character sheet", "character development & background", "e-mails with the DM", "character journal", "e-mails with other party members", and "Adventure Log from DM". Both games I play in share the same DM so its easy to organize the folders the same way.
For the campaign I run, there are gazillions of folders (I'm folder happy).
* Adventures (with sub-folders for notes on each individual adventure/module I have run)
* "The Company" (with subfolders for each individual player in the campaign)
* Religion (with subfolders for each major religion)
* Character Builder (with subfolders for classes, prestige classes, and cultural/regional modifications)
* Races (with subfolders for each race)
* Countries (separate subfolders for each country with notes)
* History (timelines, etc.)
* Maps (any computer-generated maps, unless they go with an adventure, in which case they're in the adventure folder)
* Player Handbouts (including pictures of monsters I have downloaded from the WotC site)
* World Introduction/Summary
* Website Images (things I make or download for my campaign's website)
* Magic (notes in the different types of magic in the world)
I think I have more folders but I can't think of them right now.
Then I have my PDF folders (organized by company/publisher and I separate from 3E stuff from my 1E, 2E, and Basic/Expert D&D purchases, and I also have a "campaign settings" folder of old campaign settings I downloaded from SVGames or RPGNow).
Then I have my "d20 Writing" folders - one for each book I've written or am currently writing which includes not only my notes or manuscripts in Word but also any stuff I've downloaded for research and also bookmarks/favorites for websites that are helpful.
For each of these, I also have a burned CD for back-up.
For paper files... for the campaign I run I have a three-ring binder with tabs organized relatively similar to my computer files but I tend not to update it because it's so huge I hardly ever take it off the shelf any more.
I have a notebook for both PCs I run and that has tabs similar to the folders on my computer.
I also have a file box in storage with file folders with tabs for all of the old campaign settings I worked on and old characters I played, going back to Jr. High.
What can I say... I'm a Virgo. They are, uh, well. "Meticulously organized" is a polite way of putting it, I guess.