Slyflourish had a great post a few weeks ago called The Campaign Folio. He uses Smead campus folders to store all his campaign information. It's a completely analogue solution to record keeping, but it seems like a great way to keep campaign related stuff like props, tiles, and other stuff together.
I've also found Power2ool.com to be an excellent, well, tool for organizing 4E (and Gamma World) encounters. It's really bare bones, but sometimes that's all you need :)