Organizing your data for each project is not only essential, but will enable each project to open quickly and make porting your project to a CD or Zip drive very easy.
Develop a logical directory structure. Not every project is the same and neither are the types of data used. Projects can have shapefiles, tables, images, CAD layers, coverages, and so forth. These must be organized in a logical order for the .apr file to read them efficiently.