One of the great things about digital photography is the many ways that you can file and catalog your work.
Filing by date is as good a method as any, but if you want to be able to lay your hands on specific photos, then you really need a cataloging program like Microsoft's Expression Media. With that, you can apply captions and key words to the photos, and then search the catalog based on that.
Most photo editing software has red eye reduction, but I don't know of any that will do it automatically. It's always easier to fix problems in-camera, but if you're using a point and shoot, or the little pop up flash on your camera, you're going to be stuck with the red eye.
David Buzzard