When you first use a new pattern - or reuse an old one - cut all the pattern pieces apart. You don't have to do it neatly, but you can also trim off a lot of the unprinted paper. This will help reduce bulk in the pattern envelope later.
Once you've separated out the pieces you need for the project you're working on, refold all the unused pieces individually. Fold each piece so that it will fit back in the envelope and so that the number is clearly visible on the outside. Don't worry about the original fold lines. The focus is keeping the piece number visible:
|You can, of course, use the original folding lines if they help you in this endeavor.|
Next time you need to use this pattern, it will be simple and quick to find the pieces you need. It will also be easy to determine if any pieces are missing or if any pieces were accidentally put in the wrong envelope. It's pretty simple, but it works for me. :)